Biocatalysts and methods for the synthesis of (s)-3-(1-aminoethyl)-phenol

ABSTRACT

The present disclosure provides engineered transaminase polypeptides having improved properties as compared to naturally occurring transaminases including the ability of converting the substrate, 3′-hydroxyacetophenone to (S)-3-(1-aminoethyl)-phenol in enantiomeric excess and high percentage conversion. Also provided are polynucleotides encoding the engineered transaminases, host cells capable of expressing the engineered transaminases, and methods of using the engineered transaminases to synthesize (S)-3-(1-aminoethyl)-phenol and related compounds useful in the production of active pharmaceutical ingredients.

1. TECHNICAL FIELD

The disclosure relates to transaminase biocatalysts and processes using the biocatalysts for the preparation of (S)-3-(1-aminoethyl)-phenol and related chiral amine compounds.

2. REFERENCE TO SEQUENCE LISTING, TABLE OR COMPUTER PROGRAM

The official copy of the Sequence Listing is submitted concurrently with the specification as an ASCII formatted text file via EFS-Web, with a file name of “CX2-051USP1_ST25.txt”, a creation date of Jun. 17, 2010, and a size of 128 kilobytes. The Sequence Listing filed via EFS-Web is part of the specification and is incorporated in its entirety by reference herein.

3. BACKGROUND

The drug rivastigmine is prescribed for the treatment of dementia of the Alzheimer's type and dementia associated with Parkinson's disease. The active drug compound has the following structure, and acts as an inhibitor of the enzyme acetylcholinesterase (AChe) involved in the breakdown of neurotransmitter acetylcholine.

Inhibition of AChe increases the half-life of acetylcholine released into synaptic clefts, thereby enhancing cholinergic neurotransmission. Rivastigmine shows substantially greater inhibition of AChE in the central nervous system (CNS) compartment than in the periphery (see Polinsky, R. J., 1998, Clinical Therapeutics 20(4):634-647). Moreover, rivastigmine preferentially inhibits the 01 enzymatic form of AChE, which predominates in the brains of patients with Alzheimer's disease (AD).

Various methods have been described for synthesis of rivastigmine. U.S. Pat. No. 4,948,807 describes a process for preparation of racemic rivastigmine by reacting an m-hydroxyphenylisopropyldimethylamine or an m-hydroxyphenylethyldimethylamine with carbamoyl chloride in the presence of NaH. Process for resolution of the racemic product is described in U.S. Pat. No. 5,602,176, which involves chiral resolution using di-o,o′-p-toluoyl tartaric acid.

Patent publication WO03/101917 describes a process for preparation of rivastigmine by condensing N-ethyl-N-methyl-4-nitrophenyl carbamate, which is obtained by demethylation of [1-(3-methoxyphenyl)ethyl]dimethylamine, in the presence of base.

Patent publication WO2004/037771 describes reductive amination of 3-methoxy acetophenone in presence of dimethylamine, titanium isopropoxide and sodium borohydride to obtain [1-(3-methoxyphenyl)ethyl]dimethylamine, which is further demethylated using hydrobromic acid to obtain 3-(1-dimethylamino)phenol. This is further resolved using (S)-(+)camphor-10-sulfonic acid and reacted with carbamoyl chloride to obtain rivastigmine.

Patent publication WO2006/068386 describes a process for preparation of 3-(1-dimethylamino)phenol by subjecting (S)-3-(1-dimethylaminoethyl)phenol to N-methylation using formaldehyde/formic acid. The 3-(1-dimethylamino)phenol it is subjected to O-carbamoylation to form rivastigmine.

Patent publication WO2008/020452 describes N-methylation using paraformaldehyde in the presence of Raney Nickel and hydrogen in a suitable solvent to obtain 3-(1-(dimethylamino)ethyl)phenol (see also Hu et al., 2007, A Simple and Efficient Synthesis of (S)- and (R)-1-(3-Methoxyphenyl) Ethylamine, Lett. Org. Chem. 4(2):126-128).

Enzyme based synthesis of rivastigmine is described in Mangas-Sanchez, 2009, Chemoenzymatic Synthesis of Rivastigmine Based on Lipase-Catalyzed Processes,” J. Org. Chem., 74 (15):5304-5310. The described process uses a lipase for the acetylation of 1-(3-methoxyphenyl)ethanol or 1-(3-methoxyphenyl)ethylamine. The desired isomer is isolated and chemically converted to (S)-1-(3-methoxyphenyl)ethanol or (S)-1-(3-methoxyphenyl)ethylamine and then to (S)-3-(1-dimethylamino)phenol.

There is a need for improved transaminase biocatalysts that can be used to prepare the intermediate compounds for making rivastigmine, related chiral amine compounds, and new processes employing those biocatalysts that are simple, cost effective, non-hazardous, and commercially viable.

4. SUMMARY

The present disclosure provides engineered polypeptides having transaminase activity, polynucleotides encoding the polypeptides, methods of the making the polypeptides, and methods of using the polypeptides for the biocatalytic conversion of the ketone substrate, 3-hydroxyacetophenone (compound (1) below) to the chiral amine product, (S)-3-(1-aminoethyl)-phenol (compound (2)) as shown in Scheme 1.

While naturally occurring transaminase polypeptides do not efficiently convert compound (1) to compound (2), the non-naturally occurring, engineered, transaminase polypeptides of the present disclosure are capable of carrying out this conversion with improved properties including, high enantiomeric excess (e.g., at least about 99% e.e.), increased activity (e.g., at least about 2-fold increased activity relative to the reference polypeptide SEQ ID NO:2), higher percent conversion (e.g., at least about 90% conversion in 24 h), in the presence of high substrate loadings (e.g., at least about 30 g/L compound (1)), and using only isopropylamine as an amino donor.

The engineered transaminase polypeptides of the present disclosure capable of converting compound (1) to compound (2) in enantiomeric excess with at least 2-fold, at least 5-fold, at least 10-fold, at least 25-fold, or at least 50-fold increased activity relative to the activity of the reference polypeptide of SEQ ID NO: 2, are synthetic variants of a naturally occurring transaminase of Vibrio fluvialis, and comprise amino acid sequences that have one or more residue differences as compared to the reference sequence of SEQ ID NO:2. The residue differences occur at residue positions that affect functional properties of the enzyme including activity (e.g., percent conversion of substrate to product), stereoselectivity, substrate and/or product binding (e.g., resistance to substrate and/or product inhibition), thermostability, solvent stability, expression, or various combinations thereof. Accordingly, in some embodiments, the polypeptides of the disclosure can have one or more residue differences as compared to SEQ ID NO:2 at the following residue positions: X18, X21, X31, X113, X122, X130, X133, X146, X147, X153, X163, X164, X167, X168, X174, X233; X235, X244, X286; X293, X316, X318; X323, X332, X375, X383, X418, X424, and X427. Additionally, the engineered transaminase polypeptides can comprise amino acid sequences with one or more amino acid residue differences as compared to SEQ ID NO: 2 that are associated with increased thermal and/or solvent stability at positions: X9, X45, X86, X177, X211, X294, X324, and X391. Amino acid residues that can be present at these positions are described in detail in the descriptions herein.

In some embodiments, the present invention provides an engineered transaminase polypeptide capable of converting 3-hydroxyacetophenone (compound (1)) to (S)-3-(1-aminoethyl)-phenol (compound (2)), wherein the transaminase polypeptide comprising an amino acid sequence having at least 80% sequence identity to SEQ ID NO: 2 and amino acid residue differences as compared to SEQ ID NO:2 at one or more positions selected from X18, X163, X235, X244, X323, X383, X424, and X427. In some embodiments, the amino acid residue differences as compared to SEQ ID NO: 2 are selected from the following: residue at position X18 is A; residue at position X163 is F or H; residue at position X235 is P; residue at position X244 is T; residue at position X323 is T; residue at position X383 is V; residue at position X424 is A; and residue at position X427 is Y. In some embodiments, the amino acid sequence can have additional amino acid residue differences as compared to SEQ ID NO:2 at one or more of the following positions: X21, X31, X74; X113, X122, X130, X133, X146, X147, X153, X164, X167, X168, X174, X233, X245, X286, X293, X315, X316, X318, X332, X375, X394, and X418, and in some embodiments these additional amino acid residue differences as compared to SEQ ID NO: 2 are selected from the following: residue at position X21 is T; residue at position X31 is M; residue at position X74 is T; residue at position X113 is V; residue at position X122 is E; residue at position X130 is L or M; residue at position X133 is R; residue at position X146 is L; residue at position X147 is K; residue at position X153 is S; residue at position X164 is S or G; residue at position X167 is K; residue at position X168 is D or K; residue at position X174 is E; residue at position X233 is T or I; residue at position X245 is T; residue at position X286 is S; residue at position X293 is S; residue at position X312 is D; residue at position X315 is G; residue at position X316 is H; residue at position X318 is D; residue at position X332 is T; residue at position X375 is V; residue at position X394 is G; and residue at position X418 is Q. In some embodiments, the polypeptide amino acid sequence has additional amino acid residue differences as compared to SEQ ID NO:2, associated with increased stability, at one or more of the following positions: X9, X45, X86, X177, X211, X294, X324, and X391; and in some embodiments, these additional amino acid residue differences at one or more of positions X9, X45, X86, X177, X211, X294, X324, and X391 associated with increased stability is selected from the following: residue at position X9 is T; residue at position X45 is H; residue at position X86 is Y; residue at position X177 is L; residue at position X211 is K; residue at position X294 is V; residue at position X324 is G; and residue at position X391 is A.

Various combinations of the disclosed amino acid differences can be combined in the engineered polypeptides as disclosed herein and provide various improved enzyme properties. In some embodiments, the engineered transaminase polypeptide has at least 2-fold, at least 5-fold, at least 10-fold, at least 25-fold, or at least 50-fold increased rate of conversion of 3-hydroxyacetophenone to (S)-3-(1-aminoethyl)-phenol as compared to the polypeptide of SEQ ID NO: 2 under suitable reaction conditions disclosed herein, e.g., 35 g/L of 3-hydroxyacetophenone, 1.5 M isopropylamine, 1 mM pyridoxal phosphate, 5% v/v DMSO, pH 7.5, and 45° C.

In some embodiments, the present disclosure provides polynucleotides encoding the engineered transaminase polypeptides capable of converting compound (1) to compound (2), as well as expression vectors comprising the polynucleotides, and host cells capable of expressing the polynucleotides encoding the polypeptides. Accordingly, in some embodiments, the present disclosure also provides methods of manufacturing the engineered transaminase polypeptides capable of converting compound (1) to compound (2), wherein the methods comprise culturing a host cell capable of expressing a polynucleotide encoding the engineered transaminase polypeptide and isolating the polypeptide from the host cell.

In some embodiments, any of the engineered transaminase polypeptides of the present disclosure can be used in improved processes for carrying out the conversion of compound (1) to compound (2) due to their improved enzymatic properties including, production of high enantiomeric excess (e.g., at least about 99% e.e.), increased activity (e.g., at least about 2-fold increased activity relative to SEQ ID NO:2), high percent conversion (e.g., at least about 90% conversion in 24 h), in the presence of high substrate loadings (e.g., at least about 30 g/L compound (1)), and using isopropylamine as the amino donor. Accordingly, in some embodiments, the present disclosure provides methods using the engineered transaminase polypeptides for preparing compound (2) in enantiomeric excess, wherein the methods comprise: contacting compound (1) with an engineered transaminase polypeptide of the present disclosure (e.g., as described in Table 2 and elsewhere herein) in the presence of an amino donor under suitable reaction conditions. Suitable reactions conditions for the conversion of compound (1) to compound (2) using the engineered transaminase polypeptides of the present disclosure are described in greater detail below, including but not limited to ranges of pH, temperature, buffer, solvent system, substrate loading, polypeptide loading, amino donor loading, atmosphere, and reaction time.

In some embodiments, an analog of compound (2) can be prepared in enantiomeric excess from an analog of compound (1) using engineered transaminase polypeptides in the above described methods. Accordingly, in some embodiments a method for the conversion of an analog of compound (1) to an analog of compound (2) can be carried out wherein the analog of compound (1) is a compound of Formula I

wherein R is a hydroxyl protecting group, and whereby the analog of compound (2) prepared is a

In some embodiments, the method can further comprise a step of dimethylating compound (2) or an analog of compound (2) thereby forming the (S)-3-(1-(dimethylamino)ethyl)phenol (compound (3)), which is an intermediate for the preparation of rivastigmine, or an analog of compound (3)

In some embodiments, the dimethylating step comprises contacting compound (2) or the analog of compound (2) with triethylamine, formic acid, and formaldehyde, under suitable reaction conditions. In some embodiments of this further dimethylation step the suitable reaction conditions comprise about 0.8 to about 1.6, about 1.0 to about 1.5, about 1.2 to about 1.4 equivalents, or about 1.3 equivalents of triethylamine. In some embodiments of this further dimethylation step the suitable reaction conditions comprise about 10 to about 18 equivalents, or 12 to 15 equivalents, or about 13.5 equivalents of formic acid. In some embodiments of this further dimethylation step the suitable reaction conditions comprise about 7 to about 9 equivalents, about 8 to about 9 equivalents, or about 9 equivalents of formaldehyde. In some embodiments of this further dimethylation step the suitable reaction conditions comprise at temperature of about 60° C. to about 90° C., about 70° C. to about 80° C., or about 75° C. In some embodiments of this dimethylation step, the reaction conditions comprise about 1.3 equivalents of TEA, about 13.5 equivalents of formic acid, about 9 equivalents of formaldehyde, and a temperature of about 75° C., and result in at least about 95%, 96%, 97%, 98%, 99% or greater conversion of compound (2) to the dimethylated product of compound (3), while optionally resulting in less than about 1%, or even less than 0.5% of a ketone byproduct of compound (1).

Additionally, the methods using the engineered transaminase polypeptides of the present disclosure to convert compound (1) to compound (2) can be used as a step in a process for the preparation of the pharmaceutical ingredient, rivastigmine (compound (4)), or its salts, hydrates, or

wherein the step in the process comprises contacting 3-hydroxyacetophenone (compound (1)) with a transaminase described herein in the presence of an amino donor under reaction conditions suitable for conversion of the 3-hydroxyacetophenone (compound (1)) to (S)-3-(1-aminoethyl)-phenol (compound (2)) in enantiomeric excess.

5. DETAILED DESCRIPTION

As used in this specification and the appended claims, the singular forms “a”, “an” and “the” include plural referents unless the context clearly indicates otherwise. Thus, for example, reference to “a polypeptide” includes more than one polypeptide.

Similarly, “comprise,” “comprises,” “comprising” “include,” “includes,” and “including” are interchangeable and not intended to be limiting.

It is to be further understood that where descriptions of various embodiments use the term “comprising,” those skilled in the art would understand that in some specific instances, an embodiment can be alternatively described using language “consisting essentially of” or “consisting of:”

It is to be understood that both the foregoing general description, including the drawings, and the following detailed description are exemplary and explanatory only and are not restrictive of this disclosure.

The section headings used herein are for organizational purposes only and not to be construed as limiting the subject matter described.

5.1 Abbreviations

The abbreviations used for the genetically encoded amino acids are conventional and are as follows:

Amino Acid Three-Letter Abbreviation One-Letter Abbreviation Alanine Ala A Arginine Arg R Asparagine Asn N Aspartate Asp D Cysteine Cys C Glutamate Glu E Glutamine Gln Q Glycine Gly G Histidine HIS H Isoleucine Ile I Leucine Leu L Lysine Lys K Methionine Met M Phenylalanine Phe F Proline Pro P Serine Ser S Threonine Thr T Tryptophan Trp W Tyrosine Tyr Y Valine Val V

When the three-letter abbreviations are used, unless specifically preceded by an “L” or a “D” or clear from the context in which the abbreviation is used, the amino acid may be in either the L- or D-configuration about α-carbon (C_(α)). For example, whereas “Ala” designates alanine without specifying the configuration about the α-carbon, “D-Ala” and “L-Ala” designate D-alanine and L-alanine, respectively. When the one-letter abbreviations are used, upper case letters designate amino acids in the L-configuration about the α-carbon and lower case letters designate amino acids in the D-configuration about the α-carbon. For example, “A” designates L-alanine and “a” designates D-alanine. When polypeptide sequences are presented as a string of one-letter or three-letter abbreviations (or mixtures thereof), the sequences are presented in the amino (N) to carboxy (C) direction in accordance with common convention.

The abbreviations used for the genetically encoding nucleosides are conventional and are as follows: adenosine (A); guanosine (G); cytidine (C); thymidine (T); and uridine (U). Unless specifically delineated, the abbreviated nucleotides may be either ribonucleosides or 2% deoxyribonucleosides. The nucleosides may be specified as being either ribonucleosides or 2′-deoxyribonucleosides on an individual basis or on an aggregate basis. When nucleic acid sequences are presented as a string of one-letter abbreviations, the sequences are presented in the 5′ to 3′ direction in accordance with common convention, and the phosphates are not indicated.

5.2 Definitions

In reference to the present disclosure, the technical and scientific terms used in the descriptions herein will have the meanings commonly understood by one of ordinary skill in the art, unless specifically defined otherwise. Accordingly, the following terms are intended to have the following meanings:

“Protein”, “polypeptide,” and “peptide” are used interchangeably herein to denote a polymer of at least two amino acids covalently linked by an amide bond, regardless of length or post-translational modification (e.g., glycosylation, phosphorylation, lipidation, myristilation, ubiquitination, etc.). Included within this definition are D- and L-amino acids, and mixtures of D- and L-amino acids.

“Aminotransferase” and “transaminase” are used interchangeably herein to refer to a polypeptide having an enzymatic capability of transferring an amino group (NH2), a pair of electrons, and a proton from a primary amine to a carbonyl group (C═O) of an acceptor molecule. Transaminases as used herein include naturally occurring (wild type) transaminase as well as non-naturally occurring engineered polypeptides generated by human manipulation.

“Amino acceptor” and “amine acceptor,” “keto substrate,” “keto,” and “ketone” are used interchangeably herein to refer to a carbonyl (keto, or ketone) compound which accepts an amino group from a donor amine. Amino acceptors are molecules of general Formula III,

in which each of R¹, R², when taken independently, is an alkyl, an alkylaryl group, or aryl group which is unsubstituted or substituted with one or more enzymatically acceptable groups. R¹ may be the same or different from R² in structure or chirality. In some embodiments, R¹ and R², taken together, may form a ring that is unsubstituted, substituted, or fused to other rings. Amino acceptors include keto carboxylic acids and alkanones (ketones). Typical keto carboxylic acids are α-keto carboxylic acids such as glyoxalic acid, pyruvic acid, oxaloacetic acid, and the like, as well as salts of these acids Amino acceptors also include substances which are converted to an amino acceptor by other enzymes or whole cell processes, such as fumaric acid (which can be converted to oxaloacetic acid), glucose (which can be converted to pyruvate), lactate, maleic acid, and others. Amino acceptors that can be used include, by way of example and not limitation, 3,4-dihydronaphthalen-1(211)-one, 1-phenylbutan-2-one, 3,3-dimethylbutan-2-one, octan-2-one, ethyl 3-oxobutanoate, 4-phenylbutan-2-one, 1-(4-bromophenyl)ethanone, 2-methyl-cyclohexamone, 7-methoxy-2-tetralone, 1-hydroxybutan-2-one, pyruvic acid, acetophenone, 3′-hydroxyacetophenone, 2-methoxy-5-fluoroacetophenone, levulinic acid, 1-phenylpropan-1-one, 1-(4-bromophenyl)propan-1-one, 1-(4-nitrophenyl)propan-1-one, 1-phenylpropan-2-one, 2-oxo-3-methylbutanoic acid, 1-(3-trifluoromethylphenyl)propan-1-one, hydroxypropanone, methoxyoxypropanone, 1-phenylbutan-1-one, 1-(2,5-dimethoxy-4-methylphenyl)butan-2-one, 1-(4-hydroxyphenyl)butan-3-one, 2-acetylnaphthalene, phenylpyruvic acid, 2-ketoglutaric acid, and 2-ketosuccinic acid, including both (R) and (S) single isomers where possible.

“Amino donor” or “amine donor” refers to an amino compound which donates an amino group to the amino acceptor, thereby becoming a carbonyl species. Amino donors are molecules of general Formula IV,

in which each of R³, R⁴, when taken independently, is an alkyl, an alkylaryl group, or aryl group which is unsubstituted or substituted with one or more enzymatically non-inhibiting groups. R³ can be the same or different from R⁴ in structure or chirality. In some embodiments, R³ and R⁴, taken together, may form a ring that is unsubstituted, substituted, or fused to other rings. Typical amino donors that can be used with the invention include chiral and achiral amino acids, and chiral and achiral amines. Amino donors that can be used with the invention include, by way of example and not limitation, isopropylamine (also referred to as 2-aminopropane), α-phenethylamine (also termed 1-phenylethanamine), and its enantiomers (S)-1-phenylethanamine and (R)-1-phenylethanamine, 2-amino-4-phenylbutane, glycine, L-glutamic acid, L-glutamate, monosodium glutamate, L-alanine, D-alanine, D,L-alanine, L-aspartic acid, L-lysine, D,L-ornithine, β-alanine, taurine, n-octylamine, cyclohexylamine, 1,4-butanediamine (also referred to as putrescine), 1,6-hexanediamine, 6-aminohexanoic acid, 4-aminobutyric acid, tyramine, and benzyl amine, 2-aminobutane, 2-amino-1-butanol, 1-amino-1-phenylethane, 1-amino-1-(2-methoxy-5-fluorophenyl)ethane, 1-amino-1-phenylpropane, 1-amino-1-(4-hydroxyphenyl)propane, 1-amino-1-(4-bromophenyl)propane, 1-amino-1-(4-nitrophenyl)propane, 1-phenyl-2-aminopropane, 1-(3-trifluoromethylphenyl)-2-aminopropane, 2-aminopropanol, 1-amino-1-phenylbutane, 1-phenyl-2-aminobutane, 1-(2,5-dimethoxy-4-methylphenyl)-2-aminobutane, 1-phenyl-3-aminobutane, 1-(4-hydroxyphenyl)-3-aminobutane, 1-amino-2-methylcyclopentane, 1-amino-3-methylcyclopentane, 1-amino-2-methylcyclohexane, 1-amino-1-(2-naphthyl)ethane, 3-methylcyclopentylamine, 2-methylcyclopentylamine, 2-ethylcyclopentylamine, 2-methylcyclohexylamine, 3-methylcyclohexylamine, 1-aminotetralin, 2-aminotetralin, 2-amino-5-methoxytetralin, and 1-aminoindan, including both (R) and (S) single isomers where possible and including all possible salts of the amines.

“Chiral amine” refers to amines of general formula R¹—CH(NH₂)—R² and is employed herein in its broadest sense, including a wide variety of aliphatic and alicyclic compounds of different, and mixed, functional types, characterized by the presence of a primary amino group bound to a secondary carbon atom which, in addition to a hydrogen atom, carries either (i) a divalent group forming a chiral cyclic structure, or (ii) two substituents (other than hydrogen) differing from each other in structure or chirality. Divalent groups forming a chiral cyclic structure include, for example, 2-methylbutane-1,4-diyl, pentane-1,4-diyl,hexane-1,4-diyl, hexane-1,5-diyl, 2-methylpentane-1,5-diyl. The two different substituents on the secondary carbon atom (R¹ and R² above) also can vary widely and include alkyl, aralkyl, aryl, halo, hydroxy, lower alkyl, lower alkoxy, lower alkylthio, cycloalkyl, carboxy, carbalkoxy, carbamoyl, mono- and di-(lower alkyl) substituted carbamoyl, trifluoromethyl, phenyl, nitro, amino, mono- and di-(lower alkyl) substituted amino, alkylsulfonyl, arylsulfonyl, alkylcarboxamido, arylcarboxamido, etc., as well as alkyl, aralkyl, or aryl substituted by the foregoing.

“Pyridoxal-phosphate,” “PLP,” “pyridoxal-5′-phosphate,” “PYP,” and “P5P” are used interchangeably herein to refer to the compound that acts as a coenzyme in transaminase reactions. In some embodiments, pyridoxal phosphate is defined by the structure 1-(4′-formyl-3′-hydroxy-2′-methyl-5′-pyridyl)methoxyphosphonic acid, CAS number [54-47-7], Pyridoxal-5′-phosphate can be produced in vivo by phosphorylation and oxidation of pyridoxol (also known as Vitamin B₆). In transamination reactions using transaminase enzymes, the amine group of the amino donor is transferred to the coenzyme to produce a keto byproduct, while pyridoxal-5′-phosphate is converted to pyridoxamine phosphate. Pyridoxal-5′-phosphate is regenerated by reaction with a different keto compound (the amino acceptor). The transfer of the amine group from pyridoxamine phosphate to the amino acceptor produces a chiral amine and regenerates the coenzyme. In some embodiments, the pyridoxal-5′-phosphate can be replaced by other members of the vitamin B₆ family, including pyridoxine (PN), pyridoxal (PL), pyridoxamine (PM), and their phosphorylated counterparts; pyridoxine phosphate (PNP), and pyridoxamine phosphate (PMP).

“Coding sequence” refers to that portion of a nucleic acid (e.g., a gene) that encodes an amino acid sequence of a protein.

“Naturally-occurring” or “wild-type” refers to the form found in nature. For example, a naturally occurring or wild-type polypeptide or polynucleotide sequence is a sequence present in an organism that can be isolated from a source in nature and which has not been intentionally modified by human manipulation.

“Recombinant” or “engineered” or “non-naturally occurring” when used with reference to, e.g., a cell, nucleic acid, or polypeptide, refers to a material, or a material corresponding to the natural or native form of the material, that has been modified in a manner that would not otherwise exist in nature, or is identical thereto but produced or derived from synthetic materials and/or by manipulation using recombinant techniques. Non-limiting examples include, among others, recombinant cells expressing genes that are not found within the native (non-recombinant) form of the cell or express native genes that are otherwise expressed at a different level.

“Percentage of sequence identity” and “percentage homology” are used interchangeably herein to refer to comparisons among polynucleotides and polypeptides, and are determined by comparing two optimally aligned sequences over a comparison window, wherein the portion of the polynucleotide or polypeptide sequence in the comparison window may comprise additions or deletions (i.e., gaps) as compared to the reference sequence for optimal alignment of the two sequences. The percentage may be calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison and multiplying the result by 100 to yield the percentage of sequence identity. Alternatively, the percentage may be calculated by determining the number of positions at which either the identical nucleic acid base or amino acid residue occurs in both sequences or a nucleic acid base or amino acid residue is aligned with a gap to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison and multiplying the result by 100 to yield the percentage of sequence identity. Those of skill in the art appreciate that there are many established algorithms available to align two sequences. Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith and Waterman, 1981, Adv. Appl. Math. 2:482, by the homology alignment algorithm of Needleman and Wunsch, 1970, J. Mol. Biol. 48:443, by the search for similarity method of Pearson and Lipman, 1988, Proc. Natl. Acad. Sci. USA 85:2444, by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the GCG Wisconsin Software Package), or by visual inspection (see generally, Current Protocols in Molecular Biology, F. M. Ausubel et al., eds., Current Protocols, a joint venture between Greene Publishing Associates, Inc. and John Wiley & Sons, Inc., (1995 Supplement) (Ausubel)). Examples of algorithms that are suitable for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al., 1990, J. Mol. Biol. 215: 403-410 and Altschul et al., 1977, Nucleic Acids Res. 3389-3402, respectively. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information website. This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as, the neighborhood word score threshold (Altschul et al, supra). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are then extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0) and N (penalty score for mismatching residues; always <0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) of 10, M-5, N=−4, and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff and Henikoff, 1989, Proc Natl Acad Sci USA 89:10915). Exemplary determination of sequence alignment and % sequence identity can employ the BESTFIT or GAP programs in the GCG Wisconsin Software package (Accelrys, Madison Wis.), using default parameters provided.

“Reference sequence” refers to a defined sequence used as a basis for a sequence comparison. A reference sequence may be a subset of a larger sequence, for example, a segment of a full-length gene or polypeptide sequence. Generally, a reference sequence is at least 20 nucleotide or amino acid residues in length, at least 25 residues in length, at least 50 residues in length, or the full length of the nucleic acid or polypeptide. Since two polynucleotides or polypeptides may each (1) comprise a sequence (i.e., a portion of the complete sequence) that is similar between the two sequences, and (2) may further comprise a sequence that is divergent between the two sequences, sequence comparisons between two (or more) polynucleotides or polypeptide are typically performed by comparing sequences of the two polynucleotides or polypeptides over a “comparison window” to identify and compare local regions of sequence similarity. In some embodiments, a “reference sequence” can be based on a primary amino acid sequence, where the reference sequence is a sequence that can have one or more changes in the primary sequence. For instance, a “reference sequence based on SEQ ID NO:2 having at the residue corresponding to X9 a threonine” refers to a reference sequence in which the corresponding residue at X9 in SEQ ID NO:2, which is a alanine, has been changed to threonine.

“Comparison window” refers to a conceptual segment of at least about 20 contiguous nucleotide positions or amino acids residues wherein a sequence may be compared to a reference sequence of at least 20 contiguous nucleotides or amino acids and wherein the portion of the sequence in the comparison window may comprise additions or deletions (i.e., gaps) of 20 percent or less as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The comparison window can be longer than 20 contiguous residues, and includes, optionally 30, 40, 50, 100, or longer windows.

“Substantial identity” refers to a polynucleotide or polypeptide sequence that has at least 80 percent sequence identity, at least 85 percent identity and 89 to 95 percent sequence identity, more usually at least 99 percent sequence identity as compared to a reference sequence over a comparison window of at least 20 residue positions, frequently over a window of at least 30-50 residues, wherein the percentage of sequence identity is calculated by comparing the reference sequence to a sequence that includes deletions or additions which total 20 percent or less of the reference sequence over the window of comparison. In specific embodiments applied to polypeptides, the term “substantial identity” means that two polypeptide sequences, when optimally aligned, such as by the programs GAP or BESTFIT using default gap weights, share at least 80 percent sequence identity, preferably at least 89 percent sequence identity, at least 95 percent sequence identity or more (e.g., 99 percent sequence identity). Preferably, residue positions which are not identical differ by conservative amino acid substitutions.

“Corresponding to”, “reference to” or “relative to” when used in the context of the numbering of a given amino acid or polynucleotide sequence refers to the numbering of the residues of a specified reference sequence when the given amino acid or polynucleotide sequence is compared to the reference sequence. In other words, the residue number or residue position of a given polymer is designated with respect to the reference sequence rather than by the actual numerical position of the residue within the given amino acid or polynucleotide sequence. For example, a given amino acid sequence, such as that of an engineered transaminase, can be aligned to a reference sequence by introducing gaps to optimize residue matches between the two sequences. In these cases, although the gaps are present, the numbering of the residue in the given amino acid or polynucleotide sequence is made with respect to the reference sequence to which it has been aligned.

“Amino acid difference” or “residue difference” refers to a change in the amino acid residue at a position of a polypeptide sequence relative to the amino acid residue at a corresponding position in a reference sequence. The positions of amino acid differences generally are referred to herein as “Xn,” where n refers to the corresponding position in the reference sequence upon which the residue difference is based. For example, a “residue difference at position X3 as compared to SEQ ID NO: 2” refers to a change of the amino acid residue at the polypeptide position corresponding to position 3 of SEQ ID NO:2. Thus, if the reference polypeptide of SEQ ID NO: 2 has a glutamine at position 3, then a “residue difference at position X3 as compared to SEQ ID NO:2” an amino acid substitution of any residue other than glutamine at the position of the polypeptide corresponding to position 3 of SEQ ID NO: 2. In most instances herein, the specific amino acid residue difference at a position is indicated as “XnY” where “Xn” specified the corresponding position as described above, and “Y” is the single letter identifier of the amino acid found in the engineered polypeptide (i.e., the different residue than in the reference polypeptide). In some instances (e.g., in Table 2), the present disclosure also provides specific amino acid differences denoted by the conventional notation “AnB”, where A is the single letter identifier of the residue in the reference sequence, “n” is the number of the residue position in the reference sequence, and B is the single letter identifier of the residue substitution in the sequence of the engineered polypeptide. In some instances, a polypeptide of the present disclosure can include one or more amino acid residue differences relative to a reference sequence, which is indicated by a list of the specified positions where changes are made relative to the reference sequence. The present disclosure includes engineered polypeptide sequences comprising one or more amino acid differences that include either/or both conservative and non-conservative amino acid substitutions.

“Conservative amino acid substitution” refers to a substitution of a residue with a different residue having a similar side chain, and thus typically involves substitution of the amino acid in the polypeptide with amino acids within the same or similar defined class of amino acids. By way of example and not limitation, an amino acid with an aliphatic side chain may be substituted with another aliphatic amino acid, e.g., alanine, valine, leucine, and isoleucine; an amino acid with hydroxyl side chain is substituted with another amino acid with a hydroxyl side chain, e.g., serine and threonine; an amino acids having aromatic side chains is substituted with another amino acid having an aromatic side chain, e.g., phenylalanine, tyrosine, tryptophan, and histidine; an amino acid with a basic side chain is substituted with another amino acid with a basis side chain, e.g., lysine and arginine; an amino acid with an acidic side chain is substituted with another amino acid with an acidic side chain, e.g., aspartic acid or glutamic acid; and a hydrophobic or hydrophilic amino acid is replaced with another hydrophobic or hydrophilic amino acid, respectively. Exemplary conservative substitutions are provided in Table 1 below.

TABLE 1 Residue Possible Conservative Substitutions A, L, V, I Other aliphatic (A, L, V, I) Other non-polar (A, L, V, I, G, M) G, M Other non-polar (A, L, V, I, G, M) D, E Other acidic (D, E) K, R Other basic (K, R) N, Q, S, T Other polar H, Y, W, F Other aromatic (H, Y, W, F) C, P None

“Non-conservative substitution” refers to substitution of an amino acid in the polypeptide with an amino acid with significantly differing side chain properties. Non-conservative substitutions may use amino acids between, rather than within, the defined groups and affects (a) the structure of the peptide backbone in the area of the substitution (e.g., proline for glycine) (b) the charge or hydrophobicity, or (c) the bulk of the side chain. By way of example and not limitation, an exemplary non-conservative substitution can be an acidic amino acid substituted with a basic or aliphatic amino acid; an aromatic amino acid substituted with a small amino acid; and a hydrophilic amino acid substituted with a hydrophobic amino acid.

“Deletion” refers to modification to the polypeptide by removal of one or more amino acids from the reference polypeptide. Deletions can comprise removal of 1 or more amino acids, 2 or more amino acids, 5 or more amino acids, 10 or more amino acids, 15 or more amino acids, or 20 or more amino acids, up to 10% of the total number of amino acids, or up to 20% of the total number of amino acids making up the reference enzyme while retaining enzymatic activity and/or retaining the improved properties of an engineered transaminase enzyme. Deletions can be directed to the internal portions and/or terminal portions of the polypeptide. In various embodiments, the deletion can comprise a continuous segment or can be discontinuous.

“Insertion” refers to modification to the polypeptide by addition of one or more amino acids from the reference polypeptide. In some embodiments, the improved engineered transaminase enzymes comprise insertions of one or more amino acids to the naturally occurring transaminase polypeptide as well as insertions of one or more amino acids to other improved transaminase polypeptides. Insertions can be in the internal portions of the polypeptide, or to the carboxy or amino terminus. Insertions as used herein include fusion proteins as is known in the art. The insertion can be a contiguous segment of amino acids or separated by one or more of the amino acids in the naturally occurring polypeptide.

“Fragment” as used herein refers to a polypeptide that has an amino-terminal and/or carboxy-terminal deletion, but where the remaining amino acid sequence is identical to the corresponding positions in the sequence. Fragments can be at least 14 amino acids long, at least 20 amino acids long, at least 50 amino acids long or longer, and up to 70%, 80%, 90%, 95%, 98%, and 99% of the full-length transaminase polypeptide, for example the polypeptide of SEQ ID NO:2 or engineered transaminase of SEQ ID NO:34.

“Isolated polypeptide” refers to a polypeptide which is substantially separated from other contaminants that naturally accompany it, e.g., protein, lipids, and polynucleotides. The term embraces polypeptides which have been removed or purified from their naturally-occurring environment or expression system (e.g., host cell or in vitro synthesis). The improved transaminase enzymes may be present within a cell, present in the cellular medium, or prepared in various forms, such as lysates or isolated preparations. As such, in some embodiments, the improved transaminase enzyme can be an isolated polypeptide.

“Substantially pure polypeptide” refers to a composition in which the polypeptide species is the predominant species present (i.e., on a molar or weight basis it is more abundant than any other individual macromolecular species in the composition), and is generally a substantially purified composition when the object species comprises at least about 50 percent of the macromolecular species present by mole or % weight. Generally, a substantially pure transaminase composition will comprise about 60% or more, about 70% or more, about 80% or more, about 90% or more, about 95% or more, and about 98% or more of all macromolecular species by mole or % weight present in the composition. In some embodiments, the object species is purified to essential homogeneity (i.e., contaminant species cannot be detected in the composition by conventional detection methods) wherein the composition consists essentially of a single macromolecular species. Solvent species, small molecules (<500 Daltons), and elemental ion species are not considered macromolecular species. In some embodiments, the isolated improved transaminases polypeptide is a substantially pure polypeptide composition.

“Stereoselectivity” refers to the preferential formation in a chemical or enzymatic reaction of one stereoisomer over another. Stereoselectivity can be partial, where the formation of one stereoisomer is favored over the other, or it may be complete where only one stereoisomer is formed. When the stereoisomers are enantiomers, the stereoselectivity is referred to as enantioselectivity, the fraction (typically reported as a percentage) of one enantiomer in the sum of both. It is commonly alternatively reported in the art (typically as a percentage) as the enantiomeric excess (e.e.) calculated therefrom according to the formula [major enantiomer−minor enantiomer]/[major enantiomer+minor enantiomer]. Where the stereoisomers are diastereoisomers, the stereoselectivity is referred to as diastereoselectivity, the fraction (typically reported as a percentage) of one diastereomer in a mixture of two diasteromers, commonly alternatively reported as the diastereomeric excess (d.e.). Enantiomeric excess and diastereomeric excess are types of stereomeric excess. “Highly stereoselective” refers to a transaminase polypeptide that is capable of converting the substrate to the corresponding chiral amine product with at least about 85% stereomeric excess.

“Improved enzyme property” refers to a transaminase polypeptide that exhibits an improvement in any enzyme property as compared to a reference transaminase. For the engineered transaminase polypeptides described herein, the comparison is generally made to the wild-type transaminase enzyme, although in some embodiments, the reference transaminase can be another improved engineered transaminase. Enzyme properties for which improvement is desirable include, but are not limited to, enzymatic activity (which can be expressed in terms of percent conversion of the substrate), thermo stability, solvent stability, pH activity profile, cofactor requirements, refractoriness to inhibitors (e.g., substrate or product inhibition), stereospecificity, and stereoselectivity (including enantioselectivity).

“Increased enzymatic activity” refers to an improved property of the engineered transaminase polypeptides, which can be represented by an increase in specific activity (e.g., product produced/time/weight protein) or an increase in percent conversion of the substrate to the product (e.g., percent conversion of starting amount of substrate to product in a specified time period using a specified amount of transaminase) as compared to the reference transaminase enzyme. Exemplary methods to determine enzyme activity are provided in the Examples. Any property relating to enzyme activity may be affected, including the classical enzyme properties of K_(max), V_(max) or k_(cat), changes of which can lead to increased enzymatic activity. Improvements in enzyme activity can be from about 1.1 times the enzymatic activity of the corresponding wild-type transaminase enzyme, to as much as 2 times, 5 times, 10 times, 20 times, 25 times, 50 times, 75 times, 100 times, or more enzymatic activity than the naturally occurring transaminase or another engineered transaminase from which the transaminase polypeptides were derived. In specific embodiments, the engineered transaminase enzyme exhibits improved enzymatic activity in the range of 1.5 to 50 times, 1.5 to 100 times greater than that of the parent transaminase enzyme. It is understood by the skilled artisan that the activity of any enzyme is diffusion limited such that the catalytic turnover rate cannot exceed the diffusion rate of the substrate, including any required cofactors. The theoretical maximum of the diffusion limit, or k_(cat)/K_(m), is generally about 10⁸ to 10⁹ (M⁻¹ s⁻¹) Hence, any improvements in the enzyme activity of the transaminase will have an upper limit related to the diffusion rate of the substrates acted on by the transaminase enzyme. Transaminase activity can be measured by any one of standard assays, such as by monitoring changes in spectrophotometric properties of reactants or products. In some embodiments, the amount of products produced can be measured by High-Performance Liquid Chromatography (HPLC) separation combined with UV absorbance or fluorescent detection following o-phthaldialdehyde (OPA) derivitization. Comparisons of enzyme activities are made using a defined preparation of enzyme, a defined assay under a set condition, and one or more defined substrates, as further described in detail herein. Generally, when lysates are compared, the numbers of cells and the amount of protein assayed are determined as well as use of identical expression systems and identical host cells to minimize variations in amount of enzyme produced by the host cells and present in the lysates.

“Conversion” refers to the enzymatic conversion of the substrate(s) to the corresponding product(s). “Percent conversion” refers to the percent of the substrate that is converted to the product within a period of time under specified conditions. Thus, the “enzymatic activity” or “activity” of a transaminase polypeptide can be expressed as “percent conversion” of the substrate to the product.

“Thermostable” refers to a transaminase polypeptide that maintains similar activity (more than 60% to 80% for example) after exposure to elevated temperatures (e.g., 40-80° C.) for a period of time (e.g., 0.5-24 hrs) compared to the wild-type enzyme.

“Solvent stable” refers to a transaminase polypeptide that maintains similar activity (more than e.g., 60% to 80%) after exposure to varying concentrations (e.g., 5-99%) of solvent (ethanol, isopropyl alcohol, dimethylsulfoxide (DMSO), tetrahydrofuran, 2-methyltetrahydrofuran, acetone, toluene, butyl acetate, methyl tert-butyl ether, etc.) for a period of time (e.g., 0.5-24 hrs) compared to the wild-type enzyme.

“Thermo- and solvent stable” refers to a transaminase polypeptide that is both thermostable and solvent stable.

“Derived from” as used herein in the context of engineered transaminase enzymes, identifies the originating transaminase enzyme, and/or the gene encoding such transaminase enzyme, upon which the engineering was based. For example, the engineered transaminase enzyme of SEQ ID NO:34 was obtained by artificially evolving, over multiple generations the gene encoding the Vibrio fluvialis transaminase enzyme of SEQ ID NO:2. Thus, this engineered transaminase enzyme is “derived from” the wild-type transaminase of SEQ ID NO:2.

“Hydrophilic Amino Acid or Residue” refers to an amino acid or residue having a side chain exhibiting a hydrophobicity of less than zero according to the normalized consensus hydrophobicity scale of Eisenberg et al., 1984, J. Mol. Biol. 179:125-142. Genetically encoded hydrophilic amino acids include L-Thr (T), L-Ser (S), L-His (H), L-Glu (E), L-Asn (N), L-Gln (O), L-Asp (D), L-Lys (K) and L-Arg (R).

“Acidic Amino Acid or Residue” refers to a hydrophilic amino acid or residue having a side chain exhibiting a pK value of less than about 6 when the amino acid is included in a peptide or polypeptide. Acidic amino acids typically have negatively charged side chains at physiological pH due to loss of a hydrogen ion. Genetically encoded acidic amino acids include L-Glu (E) and L-Asp (D).

“Basic Amino Acid or Residue” refers to a hydrophilic amino acid or residue having a side chain exhibiting a pK value of greater than about 6 when the amino acid is included in a peptide or polypeptide. Basic amino acids typically have positively charged side chains at physiological pH due to association with hydronium ion. Genetically encoded basic amino acids include L-Arg (R) and L-Lys (K).

“Polar Amino Acid or Residue” refers to a hydrophilic amino acid or residue having a side chain that is uncharged at physiological pH, but which has at least one bond in which the pair of electrons shared in common by two atoms is held more closely by one of the atoms. Genetically encoded polar amino acids include L-Asn (N), L-Gln (Q), L-Ser (S) and L-Thr (T).

“Hydrophobic Amino Acid or Residue” refers to an amino acid or residue having a side chain exhibiting a hydrophobicity of greater than zero according to the normalized consensus hydrophobicity scale of Eisenberg et al., 1984, J. Mol. Biol. 179:125-142. Genetically encoded hydrophobic amino acids include L-Pro (P), L-Ile (I), L-Phe (F), L-Val (V), L-Leu (L), L-Trp (W), L-Met (M), L-Ala (A) and L-Tyr (Y).

“Aromatic Amino Acid or Residue” refers to a hydrophilic or hydrophobic amino acid or residue having a side chain that includes at least one aromatic or heteroaromatic ring. Genetically encoded aromatic amino acids include L-Phe (F), L-Tyr (Y) and L-Trp (W). Although owing to the pKa of its heteroaromatic nitrogen atom L-His (H) it is sometimes classified as a basic residue, or as an aromatic residue as its side chain includes a heteroaromatic ring, herein histidine is classified as a hydrophilic residue or as a “constrained residue” (see below).

“Constrained Amino Acid or Residue” refers to an amino acid or residue that has a constrained geometry. Herein, constrained residues include L-pro (P) and L-his (H). Histidine has a constrained geometry because it has a relatively small imidazole ring. Proline has a constrained geometry because it also has a five membered ring.

“Non-polar Amino Acid or Residue” refers to a hydrophobic amino acid or residue having a side chain that is uncharged at physiological pH and which has bonds in which the pair of electrons shared in common by two atoms is generally held equally by each of the two atoms (i.e., the side chain is not polar). Genetically encoded non-polar amino acids include L-Gly (G), L-Leu (L), L-Val (V), L-Ile (I), L-Met (M) and L-Ala (A).

“Aliphatic Amino Acid or Residue” refers to a hydrophobic amino acid or residue having an aliphatic hydrocarbon side chain. Genetically encoded aliphatic amino acids include L-Ala (A), L-Val (V), L-Leu (L) and L-Ile (I).

“Cysteine” represented by L-Cys (C) is unusual in that it can form disulfide bridges with other L-Cys (C) amino acids or other sulfanyl- or sulfhydryl-containing amino acids. The “cysteine-like residues” include cysteine and other amino acids that contain sulfhydryl moieties that are available for formation of disulfide bridges. The ability of L-Cys (C) (and other amino acids with —SH containing side chains) to exist in a peptide in either the reduced free —SH or oxidized disulfide-bridged form affects whether L-Cys (C) contributes net hydrophobic or hydrophilic character to a peptide. While L-Cys (C) exhibits a hydrophobicity of 0.29 according to the normalized consensus scale of Eisenberg (Eisenberg et al., 1984, supra), it is to be understood that for purposes of the present disclosure L-Cys (C) is categorized into its own unique group.

“Small Amino Acid or Residue” refers to an amino acid or residue having a side chain that is composed of a total three or fewer carbon and/or heteroatoms (excluding the α-carbon and hydrogens). The small amino acids or residues may be further categorized as aliphatic, non-polar, polar or acidic small amino acids or residues, in accordance with the above definitions. Genetically-encoded small amino acids include L-Ala (A), L-Val (V), L-Cys (C), L-Asn (N), L-Ser (S), L-Thr (T) and L-Asp (D).

“Hydroxyl-containing Amino Acid or Residue” refers to an amino acid containing a hydroxyl (—OH) moiety. Genetically-encoded hydroxyl-containing amino acids include L-Ser (S) L-Thr (T) and L-Tyr (Y).

“Stringent hybridization” is used herein to refer to conditions under which nucleic acid hybrids are stable. As known to those of skill in the art, the stability of hybrids is reflected in the melting temperature (T_(m)) of the hybrids. In general, the stability of a hybrid is a function of ion strength, temperature, G/C content, and the presence of chaotropic agents. The T_(m) values for polynucleotides can be calculated using known methods for predicting melting temperatures (see, e.g., Baldino et al., Methods Enzymology 168:761-777; Bolton et al., 1962, Proc. Natl. Acad. Sci. USA 48:1390; Bresslauer et al., 1986, Proc. Natl. Acad. Sci. USA 83:8893-8897; Freier et al., 1986, Proc. Natl. Acad. Sci. USA 83:9373-9377; Kierzek et al., Biochemistry 25:7840-7846; Rychlik et al., 1990, Nucleic Acids Res 18:6409-6412 (erratum, 1991, Nucleic Acids Res 19:698); Sambrook et al., supra); Suggs et al., 1981, In Developmental Biology Using Purified Genes (Brown et al., eds.), pp. 683-693, Academic Press; and Wetmur, 1991, Crit. Rev Biochem Mol Biol 26:227-259. All publications incorporate herein by reference). In some embodiments, the polynucleotide encodes the polypeptide disclosed herein and hybridizes under defined conditions, such as moderately stringent or highly stringent conditions, to the complement of a sequence encoding an engineered transaminase enzyme of the present disclosure.

“Hybridization stringency” relates to hybridization conditions, such as washing conditions, in the hybridization of nucleic acids. Generally, hybridization reactions are performed under conditions of lower stringency, followed by washes of varying but higher stringency. The term “moderately stringent hybridization” refers to conditions that permit target-DNA to bind a complementary nucleic acid that has about 60% identity, preferably about 75% identity, about 85% identity to the target DNA, with greater than about 90% identity to target-polynucleotide. Exemplary moderately stringent conditions are conditions equivalent to hybridization in 50% formamide, 5×Denhart's solution, 5×SSPE, 0.2% SDS at 42° C., followed by washing in 0.2×SSPE, 0.2% SDS, at 42° C. “High stringency hybridization” refers generally to conditions that are about 10° C. or less from the thermal melting temperature T_(m) as determined under the solution condition for a defined polynucleotide sequence. In some embodiments, a high stringency condition refers to conditions that permit hybridization of only those nucleic acid sequences that form stable hybrids in 0.018M NaCl at 65° C. (i.e., if a hybrid is not stable in 0.018M NaCl at 65° C., it will not be stable under high stringency conditions, as contemplated herein). High stringency conditions can be provided, for example, by hybridization in conditions equivalent to 50% formamide, 5×Denhart's solution, 5×SSPE, 0.2% SDS at 42° C., followed by washing in 0.1×SSPE, and 0.1% SDS at 65° C. Another high stringency condition is hybridizing in conditions equivalent to hybridizing in 5×SSC containing 0.1% (w:v) SDS at 65° C. and washing in 0.1×SSC containing 0.1% SDS at 65° C. Other high stringency hybridization conditions, as well as moderately stringent conditions, are described in the references cited above.

“Heterologous” polynucleotide refers to any polynucleotide that is introduced into a host cell by laboratory techniques, and includes polynucleotides that are removed from a host cell, subjected to laboratory manipulation, and then reintroduced into a host cell.

“Codon optimized” refers to changes in the codons of the polynucleotide encoding a protein to those preferentially used in a particular organism such that the encoded protein is efficiently expressed in the organism of interest. Although the genetic code is degenerate in that most amino acids are represented by several codons, called “synonyms” or “synonymous” codons, it is well known that codon usage by particular organisms is nonrandom and biased towards particular codon triplets. This codon usage bias may be higher in reference to a given gene, genes of common function or ancestral origin, highly expressed proteins versus low copy number proteins, and the aggregate protein coding regions of an organism's genome. In some embodiments, the polynucleotides encoding the transaminases enzymes may be codon optimized for optimal production from the host organism selected for expression.

“Preferred, optimal, high codon usage bias codons” refers interchangeably to codons that are used at higher frequency in the protein coding regions than other codons that code for the same amino acid. The preferred codons may be determined in relation to codon usage in a single gene, a set of genes of common function or origin, highly expressed genes, the codon frequency in the aggregate protein coding regions of the whole organism, codon frequency in the aggregate protein coding regions of related organisms, or combinations thereof. Codons whose frequency increases with the level of gene expression are typically optimal codons for expression. A variety of methods are known for determining the codon frequency (e.g., codon usage, relative synonymous codon usage) and codon preference in specific organisms, including multivariate analysis, for example, using cluster analysis or correspondence analysis, and the effective number of codons used in a gene (see GCG CodonPreference, Genetics Computer Group Wisconsin Package; CodonW, John Peden, University of Nottingham; McInerney, J. O, 1998, Bioinformatics 14:372-73; Stenico et al., 1994, Nucleic Acids Res. 222437-46; Wright, F., 1990, Gene 87:23-29). Codon usage tables are available for a growing list of organisms (see for example, Wada et al., 1992, Nucleic Acids Res. 20:2111-2118; Nakamura et al., 2000, Nucl. Acids Res. 28:292; Duret, et al., supra; Henaut and Danchin, “Escherichia coli and Salmonella,” 1996, Neidhardt, et al. Eds., ASM Press, Washington D.C., p. 2047-2066. The data source for obtaining codon usage may rely on any available nucleotide sequence capable of coding for a protein. These data sets include nucleic acid sequences actually known to encode expressed proteins (e.g., complete protein coding sequences-CDS), expressed sequence tags (ESTS), or predicted coding regions of genomic sequences (see for example, Mount, D., Bioinformatics: Sequence and Genome Analysis, Chapter 8, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 2001; Uberbacher, E. C., 1996, Methods Enzymol. 266:259-281; Tiwari et al., 1997, Comput. Appl. Biosci. 13:263-270).

“Control sequence” is defined herein to include all components, which are necessary or advantageous for the expression of a polynucleotide and/or polypeptide of the present disclosure. Each control sequence may be native or foreign to the nucleic acid sequence encoding the polypeptide. Such control sequences include, but are not limited to, a leader, polyadenylation sequence, propeptide sequence, promoter, signal peptide sequence, and transcription terminator. At a minimum, the control sequences include a promoter, and transcriptional and translational stop signals. The control sequences may be provided with linkers for the purpose of introducing specific restriction sites facilitating ligation of the control sequences with the coding region of the nucleic acid sequence encoding a polypeptide.

“Operably linked” is defined herein as a configuration in which a control sequence is appropriately placed (i.e., in a functional relationship) at a position relative to a polynucleotide of interest such that the control sequence directs or regulates the expression of the polynucleotide and/or polypeptide of interest.

“Promoter sequence” refers to a nucleic acid sequence that is recognized by a host cell for expression of a polynucleotide of interest, such as a coding sequence. The promoter sequence contains transcriptional control sequences, which mediate the expression of a polynucleotide of interest. The promoter may be any nucleic acid sequence which shows transcriptional activity in the host cell of choice including mutant, truncated, and hybrid promoters, and may be obtained from genes encoding extracellular or intracellular polypeptides either homologous or heterologous to the host cell.

5.3 Polypeptides for the Synthesis of (8)-3-(1-Aminoethyl)phenol

The present disclosure provides polypeptides having transaminase activity for the synthesis of (S)-3-(1-aminoethyl)-phenol, polynucleotides encoding the polypeptides, and methods for using the polypeptides. Where the description relates to polypeptides, it is to be understood that it also describes the polynucleotides encoding the polypeptides.

Aminotransferases, also known as transaminases, catalyze the transfer of an amino group, a pair of electrons, and a proton from a primary amine of an amino donor substrate to the carbonyl group (i.e., a keto group) of an amino acceptor molecule. Aminotransferases have been identified from various organisms, such as Alcaligenes denitrificans, Bordetella bronchiseptica, Bordetella parapertussis, Brucella melitensis, Burkholderia malle, Burkholderia pseudomallei, Chromobacterium violaceum, Oceanicola granulosus HTCC2516, Oceanobacter sp. RED65, Oceanospirillum sp. MED92, Pseudomonas putida, Ralstonia solanacearum, Rhizobium meliloti, Rhizobium sp. (strain NGR234), Vibrio fluvialis, Bacillus thuringensis, and Klebsiella pneumoniae (Shin et al., 2001, Biosci. Biotechnol, Biochem. 65:1782-1788).

The stereoselectivity of transaminases in the conversion of a ketone to the corresponding amine make these enzymes useful in the asymmetric synthesis of optically pure amines from the corresponding keto compounds (see, e.g., Höhne et al., Biocatalytic Routes to Optically Active Amines,” Chem Cat Chem 1(1):42-51; Zua and Hua, 2009, Biotechnol J. 4(10):1420-31). Transaminases can also be applied to the chiral resolution of racemic amines by exploiting the ability of the transaminases to carry out the reverse reaction in a stereospecific manner, i.e., preferential conversion of one enantiomer to the corresponding ketone, thereby resulting in a mixture enriched in the other enantiomer (see, e.g., Koselewski et al., 2009, Org. Lett. 11(21):4810-2).

U.S. application Ser. No. 12/684,864, filed Jan. 8, 2010 and International application PCT/US10/020,563, filed Jan. 9, 2010 discloses engineered transaminases derived from the naturally occurring transaminase of Vibrio fluvialis and having increased stability to temperature and/or organic solvent. These transaminases have also been adapted to have enzymatic activity towards structurally different amino acceptor molecules. Engineered transaminases derived from the transaminase of Vibrio fluvialis are also described in Cho et al., 2008, Biotechnol Bioeng. 99(2):275-84. As shown herein, it has been discovered that the transaminase polypeptides derived from V. fluvialis can mediate the transamination of 3′-hydroxyacetophenone to (S)-3-(1-aminoethyl)-phenol in enantiomeric excess. Importantly, mutations that increase the enzymatic activity and enantioselectivity of the transaminase have been identified for the development of transaminase biocatalysts for the efficient conversion of 3′-hydroxyacetophenone to (S)-3-(1-aminoethyl)-phenol in enantiomeric excess.

Accordingly, in one aspect, the present invention relates to polypeptides that are capable of converting the substrate 3′-hydroxyacetophenone (compound (1)) to the product (S)-3-(1-aminoethyl)-phenol (compound (2))

in the presence of an amino donor, where the (S)-3-(1-aminoethyl)-phenol is produced in enantiomeric excess. In some embodiments, the polypeptide is the wild-type polypeptide of V. fluvialis, as represented by the sequence of SEQ ID NO:2.

In some embodiments, the polypeptides are non-naturally occurring transaminases engineered to have increased activity as compared to the wild-type V. fluvialis polypeptide of SEQ ID NO:2, or another engineered polypeptide, for example SEQ ID NO:4. These engineered transaminase polypeptides adapted for efficient conversion of 3′-hydroxyacetophenone to the product (S)-3-(1-aminoethyl)-phenol have one or more residue differences as compared to the amino acid sequence of SEQ ID NO:2 or a reference engineered transaminase polypeptide, such as the reference polypeptide of SEQ ID NO:4. The residue differences are associated with enhancements in enzyme properties, particularly increased enzymatic activity and/or enzyme stability for the conversion of 3′-hydroxyacetophenone to (S)-3-(1-aminoethyl)-phenol.

In the embodiments herein, the engineered transaminase polypeptides show increased activity in the conversion of the substrate 3′-hydroxyacetophenone to the product (S)-3-(1-aminoethyl)-phenol product in a defined time with the same amount of enzyme as compared to the wild type or reference enzyme. In some embodiments, the engineered transaminase polypeptides has at least about 1.2 fold, 1.5 fold, 2 fold, 3 fold, 4 fold, 5 fold, 10 fold, 20 fold, 30 fold, 40 fold, 50 fold, 100 fold, or more the activity of the polypeptide represented by SEQ ID NO:4 in the conversion of 3′-hydroxyacetophenone to (S)-3-(1-aminoethyl)-phenol.

In some embodiments, the engineered polypeptide capable of converting the substrate 3′-hydroxyacetophenone to the product (S)-3-(1-aminoethyl)-phenol in enantiomeric excess comprises an amino acid sequence that is at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more identical to the reference sequence of SEQ ID NO:2, where the amino acid sequence has one or more residue differences as compared to the amino acid sequence of SEQ ID NO:2.

In some embodiments, the engineered polypeptide capable of converting the substrate 3′-hydroxyacetophenone to the product (S)-3-(1-aminoethyl)-phenol in enantiomeric excess comprises an amino acid sequence that is at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more identical to the reference sequence of SEQ ID NO:4, where the amino acid sequence has one or more residue differences as compared to the amino acid sequence of SEQ ID NO:4.

In some embodiments, the engineered polypeptide capable of converting the substrate 3′-hydroxyacetophenone to the product (S)-3-(1-aminoethyl)-phenol in enantiomeric excess comprises an amino acid sequence that is at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more identical to a reference sequence selected from SEQ ID NO:8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, and 44. In particular, the engineered transaminase polypeptide can comprise an amino acid sequence that is at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more identical to the reference sequence of SEQ ID NO: 8, 14, 18, 28, or 32.

In the embodiments herein, the engineered transaminases have one or more residue differences as compared to the amino acid sequence of SEQ ID NO:2 or a reference engineered transaminase polypeptide, such as the reference polypeptide of SEQ ID NO:4. In some embodiments, the transaminases have one or more residue differences at residue positions selected from X18, X21, X31, X113, X122, X130, X133, X146, X147, X153, X163, X164, X167, X168, X174, X233; X235, X244, X286; X293, X316, X318; X323, X332, X375, X383, X418, X424, and X427. As further described below, the transaminases can have in combination with the residue differences at the foregoing residue positions, one or more residue differences at residue positions selected from X9, X45, X86, X177, X211, X294, X324, and X391.

The residue positions X18, X86, X153, X163, X286, X316, and X323 are associated with the substrate binding, and consequently are associated with effects on enzyme activity. Accordingly, transaminases with desirable changes in enzymatic activity can be prepared by introducing one or more residue differences as compared to SEQ ID NO:2 at the foregoing residue positions.

The residue positions X21, X113, X122, X130, X133, X146, X164, X167, X168, X177, X211, X294, X316, X318, X324, X332, X375, X391 and X418 are associated with increases in stability, including thermo- and/or solvent stability. Accordingly, transaminases with desirable changes in stability to elevated temperature or solvent concentrations can be prepared by introducing one or more residue differences as compared to SEQ ID NO:2 at the foregoing residue positions.

The residue positions X31, X45, X133, and X146, are associated with tolerance to product accumulation (e.g., decrease in inhibition of enzyme activity by the specified product). Accordingly, transaminases with decreased sensitivity to product accumulation can be prepared by introducing one or more residue differences as compared to SEQ ID NO:2 at the foregoing residue positions.

The residue positions X18, X86, X147, X153, X163, X174, X233, X235, X244, X286, X323, X383, X394, X424, and X427 are associated with increases in activity with respect to the conversion of substrate 3′-hydroxyacetophenone to (S)-3-(1-aminoethyl)-phenol. As noted above, some of the residue positions are associated with substrate binding, and thus, transaminases with desirable changes enzymatic activity for the described reaction can be prepared by introducing one or more residue differences as compared to SEQ ID NO:2 at the foregoing residue positions.

The residue positions X9, X284, X287, X293, X295, X299, X300, X411, X415, and X417 are associated with increased expression of the polypeptide, particularly in a bacterial host cell, such as E. coli. Accordingly, transaminases that have desirable changes in expression levels in a host cell can be prepared by introducing one or more residue differences as compared to SEQ ID NO:2 at the forgoing residue positions.

It is to be understood that the residue differences from SEQ ID NO:2 at residue positions associated with the various properties of the enzymes can be used in various combinations to form transaminase polypeptides having desirable enzymatic characteristics, for example combination of increases in enzyme activity, solvent and temperate stability, and utilization of amino donor. Exemplary combinations are described herein.

In some embodiments, the amino acid residues for the specified residue positions can be selected based on the following: X18 is an aliphatic amino acid residue; X21 is a constrained amino acid residue; X31 is a non-polar amino acid residue; X113 is an aliphatic amino acid residue; X122 is an acidic amino acid residue; X130 is a non-polar amino acid residue; X133 is a basic amino acid residue; X146 is an aliphatic amino acid residue; X147 is a basic amino acid residue; X153 is a polar amino acid residue; X163 is a constrained or aromatic amino acid residue, X164 is a polar or non-polar amino acid residue; X167 is a basic amino acid residue; X168 is a basic or acidic amino acid residue; X174 is an acidic amino acid residue; X233 is an aliphatic or polar amino acid residue; X235 is a constrained amino acid residue; X244 is a polar amino acid residue; X286 is a polar amino acid residue; X293 is a polar amino acid residue; X316 is a constrained amino acid residue; X318 is an acidic amino acid residue; X323 is a polar amino acid residue; X332 is a polar amino acid residue; X375 is an aliphatic amino acid residue; X383 is an aliphatic amino acid residue; X418 is a polar amino acid residue; X424 is an aliphatic amino acid residue; and X427 is an aromatic amino acid residue. In some embodiments, where the amino acid residue at the corresponding residue position of the reference sequence are encompassed within the category of amino acids described for the specified position, a different amino acid within that amino acid category can be used in light of the guidance provided herein.

The amino acid residues for the other residue positions specified above can be selected from the following: X9 is a polar amino acid residue; X45 is a constrained amino acid residue; X86 is a constrained, aromatic or polar amino acid residue; X177 is an aliphatic amino acid residue; X211 is an basic amino acid residue; X294 is a non-polar or aliphatic amino acid residue; X324 is a non-polar amino acid residue, and X391 is an aliphatic amino acid residue. As above, where the amino acid residue at the corresponding residue position of the reference sequence are encompassed within the category of amino acids described for the specified position, a different amino acid within that amino acid category can be used in light of the guidance provided herein.

In accordance with the above, in some embodiments, the amino acid residues for the specified residue positions can be selected based on the following: X18 is A, V, L or I, particularly A; X21 is P or H, particularly H; X31 is G, M, A, V, L or I, particularly M; X113 is A, V, L, or I, particularly V; X122 is E; X130 is G, M, A, V, L or I, particularly L or M; X133 is R or K, particularly R; X146 is A, V, L or I, particularly L; X147 is R or K, particularly K; X153 is N, Q, S, or T, particularly S; X163 is P, H, Y, W, or F; X164 is N, Q, S, T, G, M, A, V, L or I, particularly S or G; X167 is R or K, particularly K; X168 is R, K, D, or E, particularly D or K; X174 is D or E; X233 is N, Q, S, T, A, V, L, or I, particularly T, or I; X235 is H or P, particularly P; X244 is N, Q, S, or T, particularly T; X286 is N, Q, S, or T, particularly S; X293 is N, Q, S, or T, particularly S; X312 is D or E, particularly D; X316 is H or P, particularly H; X318 is D or E, particularly D; X323 is N, Q, S, or T, particularly T; X332 is N, Q, S, or T, particularly T; X375 is A, V, or L, particularly V; X383 is A, V, L, or I, particularly V; -; X418 is N, Q, S, or T, particularly Q; X424 is A, V, L or I, particularly A, and X427 is W or Y, particularly Y.

For the other residue positions, the amino acid residues can be selected based on the following: X9 is N, Q, S, or T, particularly T; X45 is H or P, particularly H; X86 is H, P, Y, W, N, Q, S, T, particularly Y; X177 is A, V, L, or I, particularly L; X211 is K; X294 is G, A, V, L or I, particularly V; X324 is G, M, A, V, L or I, particularly G; and X391 is A, V, L or I, particularly A.

In some embodiments, the engineered transaminase polypeptide capable of converting 3-hydroxyacetophenone to (S)-3-(1-aminoethyl)-phenol comprises an amino acid sequence that has the percent identity described above and has one or more amino acid residue differences as compared to SEQ ID NO:2 at residue positions corresponding to X18, X163, X235, X244, X323, X383, X424, and X427. In some embodiments, the engineered transaminase polypeptide has at least two or more, three or more, four or more, five or more, or six or more residue differences at the specified residue positions. The amino acid residues for the indicated residue positions can be selected as described above.

In some embodiments, the transaminase polypeptide comprises an amino acid sequence having at least at residue at position X163 an aromatic or constrained amino acid residue. In some embodiments, the amino acid sequence comprises at least at the residue at position X163 an F or H.

In some embodiments, the transaminase polypeptide comprises an amino acid sequence having at least the following: residue at position X153 is a polar amino acid residue; and residue at position X177 is an aliphatic amino acid residue. In some embodiments, the transaminase amino acid sequence comprises at least the following: residue at position X153 is S; and residue at position X177 is L.

In some embodiments, the transaminase polypeptide comprises an amino acid sequence having at least the following: residue at position X18 is an aliphatic amino acid residue; residue at position X153 is a polar amino acid residue; residue at position X163 is an aromatic or constrained amino acid residue; residue at position X177 is an aliphatic amino acid residue; residue at position X235 is a constrained amino acid residue; residue at position X323 is a polar amino acid residue; and residue at position X424 is an aliphatic amino acid residue.

In some embodiments, the transaminase polypeptide comprises an amino acid sequence having at least the following: residue at position X18 is A; residue at position X153 is S; residue at position X163 is F or H; residue at position X177 is L; residue at position X235 is P; residue at position X323 is T; and residue at position X424 is A.

In some embodiments, the transaminase polypeptide comprises an amino acid sequence having at least the following: residue at position X18 is an aliphatic amino acid residue; residue at position X153 is a polar amino acid residue, residue at position X163 is an aromatic or constrained amino acid residue, residue at position X177 is an aliphatic amino acid residue, residue at position X235 is a constrained amino acid residue, residue at position X244 is a polar residue, residue at position X323 is a polar residue, residue at position X383 is an aliphatic amino acid residue, and residue at position X424 is an aliphatic amino acid residue.

In some embodiments, the transaminase polypeptide comprises an amino acid sequence having at least the following: residue at position X18 is A; residue at position X153 is S, residue at position X163 is F or H, residue at position X177 is L, residue at position X235 is P, residue at position X244 is T, residue at position X323 is T, residue at position X383 is V, and residue at position X424 is A.

In some embodiments, the transaminase polypeptide comprises an amino acid sequence having, in addition to the one or more residue differences at residue positions X18, X163, X235, X244, X323, X383, X424, and X427, one or more residue differences as compared to SEQ ID NO:2 at the following residue positions: X21, X31, X113, X122, X130; X133; X146; X147, X164; X167; X168; X174; X233; X286; X293, X316, X318, X332, X375, and X418.

In some embodiments, the transaminase polypeptide comprises an amino acid sequence having, in addition to the one or more residue differences at residue position X18, X163, X235, X244, X323, X383, X424, and X427, one or more of the following: residue at position X21 is a constrained amino acid residue; residue at position X31 is a non-polar amino acid residue; residue at position X113 is an aliphatic amino acid residue; residue at position X122 is an acidic amino acid residue; residue at position X130 is a non-polar residue; residue at position X133 is a basic amino acid residue; residue at position X146 is an aliphatic amino acid residue; residue at position X147 is a basic amino acid residue; residue at position X164 is a polar or non-polar amino acid residue; residue at position X167 is a basic amino acid residue; residue at position X168 is an acidic or basic amino acid residue; residue at position X174 is an acidic amino acid residue; residue at position X233 is a polar or aliphatic amino acid residue; -; residue at position X286 is a polar amino acid residue; residue at position X293 is a polar amino acid residue; residue at position X316 is a constrained amino acid residue; residue at position X318 is an acidic amino acid residue; residue at position X375 is an aliphatic amino acid residue; -; residue at position X418 is a polar amino acid residue; and residue at position X427 is an aromatic amino acid residue. In some embodiments, where the amino acid residue at the corresponding residue position of the reference sequence is encompassed within the category of amino acids described for the specified position, a different amino acid within that amino acid category can be used in light of the guidance provided herein.

In some embodiments, the transaminase polypeptide comprises an amino acid sequence having, in addition to residue differences at one or more of residue positions corresponding to X18, X163, X235, X244, X323, X383, X424, and X427, one or more of the following: residue at position X21 is T; residue at position X31 is M; -; residue at position X113 is V; residue at position X122 is E; residue at position X130 is L or M; residue at position X133 is R; residue at position X146 is L; residue at position X147 is K; residue at position X164 is S or G; residue at position X167 is K; residue at position X168 is D or K; residue at position X174 is E; residue at position X233 is T or I; residue at position X286 is S; residue at position X293 is S; residue at position X316 is H; residue at position X318 is D; residue at position X375 is V; -; residue at position X418 is Q; and residue at position X427 is Y.

In some embodiments, the transaminase polypeptides can have additionally one or more residue differences at residue positions not specified by an X above as compared to a reference sequence, for example SEQ ID NO:2. In some embodiments, the differences can be 1-2,1-3, 1-4,1-5, 1-6,1-7, 1-8,1-9, 1-10, 1-15, 1-20, 1-21, 1-22, 1-23, 1-24, 1-25, 1-30, 1-35, 1-40, 1-45, 1-50, 1-55, or 1-60 residue differences at other amino acid residue positions not defined by X above. In some embodiments, the number of differences can be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 30, 35, 40, 45, 50, 55, or 60 residue differences at other amino acid residue positions. In some embodiments, the differences comprise conservative mutations.

In some embodiments, the transaminase polypeptide comprises an amino acid sequence having at least the following: residue at position X153 is a polar amino acid residue, residue at position X177 is an aliphatic amino acid residue; and residue at position X233 is a polar or aliphatic residue. In some embodiments, the transaminase amino acid sequence comprises the following: residue at position X153 is S, residue at position X177 is L; and residue at position X233 is T or I.

In some embodiments, the transaminase polypeptide comprises amino acid sequence having at least the following: residue at position X153 is a polar amino acid residue, residue at position X163 is an aromatic or constrained residue; residue at position X177 is an aliphatic amino acid residue; and residue at position X233 is a polar or aliphatic residue. In some embodiments, the transaminase amino acid sequence comprises at least the following: residue at position X153 is S; residue at position X163 is F or H; residue at position X177 is L; and residue at position X233 is T or I.

In some embodiments, the transaminase polypeptide comprises an amino acid sequence having at least the following: residue at position X153 is a polar amino acid residue; residue at position X163 is an aromatic or constrained amino acid residue; residue at position X177 is an aliphatic amino acid residue; residue at position X233 is a polar or aliphatic residue; residue at position X235 is a constrained amino acid residue; residue at position X424 is an aliphatic amino acid residue; and residue at position X427 is an aromatic amino acid residue. In some embodiments, the transaminase polypeptide comprises an amino acid sequence having at least the following: residue at position X153 is S; residue at position X163 is F or H; residue at position X177 is L; residue at position X233 is T or I; residue at position X235 is P; residue at position X424 is A; and residue at position X427 is Y.

In some embodiments, the transaminase polypeptide comprises an amino acid sequence having at least the following: residue at position X18 is an aliphatic amino acid residue; residue at position X21 is a constrained amino acid residue; residue at position X153 is a polar amino acid residue; residue at position X163 is an aromatic amino acid residue; residue at position X177 is an aliphatic amino acid residue; residue at position X233 is a polar or aliphatic residue; residue at position X235 is a constrained amino acid residue; residue at position X323 is a polar amino acid residue; residue at position X383 is an aliphatic amino acid residue; residue at position X424 is an aliphatic amino acid residue; and residue at position X427 is an aromatic amino acid residue. In some embodiments, the transaminase polypeptide comprises an amino acid sequence having at least the following: residue at position X18 is A; residue at position X21 is H; residue at position X153 is S; residue at position X163 is F or H; residue at position X177 is L; residue at position X233 is T or I; residue at position X235 is P; residue at position X323 is T; residue at position X383 is V; residue at position X424 is A; and residue at position X427 is Y.

In some embodiments, the transaminase polypeptide comprises an amino acid sequence having at least the following: residue at position X18 is an aliphatic amino acid residue; residue at position X21 is constrained amino acid residue; residue at position X147 is a basic amino acid residue; residue at position X153 is a polar amino acid residue; residue at position X163 is an aromatic amino acid residue; residue at position X177 is an aliphatic amino acid residue; residue at position X233 is a polar or aliphatic residue; residue at position X235 is a constrained amino acid residue; residue at position X323 is a polar amino acid residue; residue at position X383 is an aliphatic amino acid residue; residue at position X424 is an aliphatic amino acid residue; and residue at position X427 is an aromatic amino acid residue.

In some embodiments, the transaminase polypeptide comprises an amino acid sequence having at least the following: residue at position X18 is A; residue at position X21 is H; residue at position X147 is K; residue at position X153 is S; residue at position X163 is F or H; residue at position X177 is L; residue at position X233 is T or I; residue at position X235 is P; residue at position X323 is T; residue at position X383 is V; residue at position X424 is A; and residue at position X427 is Y.

In some embodiments, the transaminase polypeptide comprises an amino acid sequence having at least the following: residue at position X18 is an aliphatic amino acid residue; residue at position X21 is constrained amino acid residue; residue at position X146 is an aliphatic amino acid residue; residue at position X147 is a basic amino acid residue; residue at position X153 is a polar amino acid residue; residue at position X163 is an aromatic amino acid residue; residue at position X177 is an aliphatic amino acid residue; residue at position X233 is a polar or aliphatic residue; residue at position X235 is a constrained amino acid residue; residue at position X323 is a polar amino acid residue; residue at position X383 is an aliphatic amino acid residue; residue at position X424 is an aliphatic amino acid residue; and residue at position X427 is an aromatic amino acid residue.

In some embodiments, the transaminase polypeptide comprises an amino acid sequence having at least the following: residue at position X18 is A; residue at position X21 is H; residue at position X146 is L; residue at position X147 is K; residue at position X153 is S; residue at position X163 is F or H; residue at position X177 is L; residue at position X233 is T or I; residue at position X235 is P; residue at position X323 is T; residue at position X383 is V; residue at position X424 is A; and residue at position X427 is Y.

In some embodiments, the transaminase polypeptide comprises an amino acid sequence having at least the following: residue at position X18 is an aliphatic amino acid residue; residue at position X21 is a constrained amino acid residue; residue at position X130 is an aliphatic or non-polar amino acid residue; residue at position X133 is a basic amino acid residue; residue at position X146 is an aliphatic amino acid residue; residue at position X147 is a basic amino acid residue; residue at position X153 is a polar amino acid residue; residue at position X163 is an aromatic amino acid residue; residue at position X177 is an aliphatic amino acid residue; residue at position X233 is a polar or aliphatic residue; residue at position X235 is a constrained amino acid residue; residue at position X323 is a polar amino acid residue; residue at position X383 is an aliphatic amino acid residue; residue at position X424 is an aliphatic amino acid residue; and residue at position X427 is an aromatic amino acid residue.

In some embodiments, the transaminase polypeptide comprises an amino acid sequence having at least the following: residue at position X18 is A; residue at position X21 is H; residue at position X130 is L or M; residue at position X133 is R; residue at position X146 is L; residue at position X147 is K; residue at position X153 is S; residue at position X163 is F; residue at position X233 is T or I; residue at position X235 is P; residue at position X323 is T; residue at position X383 is V; residue at position X424 is A; and residue at position X427 is Y.

In some embodiments, the transaminase polypeptide comprises an amino acid sequence having at least the following: residue at position X18 is an aliphatic amino acid residue; residue at position X21 is a constrained amino acid residue; residue at position X31 is a non-polar amino acid residue; residue at position X133 is a basic amino acid residue; residue at position X146 is an aliphatic amino acid residue; residue at position X147 is a basic amino acid residue; residue at position X153 is a polar amino acid residue; residue at position X163 is an aromatic or constrained amino acid residue; residue at position X233 is a polar or aliphatic residue; residue at position X235 is a constrained amino acid residue; residue at position X244 is a polar amino acid residue; residue at position X318 is an acidic amino acid residue; residue at position X323 is a polar amino acid residue; residue at position X383 is an aliphatic amino acid residue; residue at position X424 is an aliphatic amino acid residue; and residue at position X427 is an aromatic amino acid residue.

In some embodiments, the transaminase polypeptide comprises an amino acid sequence having at least the following: residue at position X18 is A; residue at position X21 is H; residue at position X31 is M; residue at position X133 is R; residue at position X146 is L; residue at position X147 is K; residue at position X153 is S; residue at position X163 is F or H; residue at position X233 is T or I; residue at position X235 is P; residue at position X244 is T; residue at position X318 is D; residue at position X323 is T; residue at position X383 is V; residue at position X424 is A; and residue at position X427 is Y.

As described above, the transaminase polypeptide can have residue differences as compared to SEQ ID NO:2, or another engineered transaminase, to improve various enzyme properties other than activity or enantioselectivity, including, among others, temperature and solvent stability. Residue positions X9, X45, X86, X177, X211, X294, X324, and X391 are associated with desirable changes in temperature and solvent stability. Accordingly, for all of the foregoing embodiments, the transaminase polypeptide can comprise an amino acid sequence that has additionally amino acid residue differences as compared to SEQ ID NO:2 at one or more of the these residue positions: X9, X45, X86, X177, X211, X294, X324, and X391. These residue positions are described in U.S. application Ser. No. 12/684,864, filed Jan. 8, 2010, incorporated herein by reference.

A significant advantage of having a thermo- and/or solvent stable transaminase as a basis for obtaining improvements in other enzyme properties, e.g., substrate recognition, enzyme activity, stereoselectivity, stereospecificity, is that the engineered transaminase can be used under a process condition that is unsuitable for the naturally occurring enzyme, for example, among others, (a) screening for activity on various substrates at conditions of elevated temperature and/or high solvent concentrations; (b) scale-up conditions where transamination reactions may be carried out for longer time periods, and/or (c) under high substrate loading conditions. In some embodiments, screening with substrate 3′-hydroxyacetophenone at the elevated temperature and/or higher solvent concentration maintains the thermo- and/or solvent stable features of the transaminase polypeptide while allowing for identification of improvements in other enzyme properties.

In some embodiments, the amino acid residue at the residue positions is selected from the following: residue at position X9 is a polar amino acid residue, residue at position X45 is a constrained amino acid residue, residue at position X86 is a cysteine, or an aliphatic, non-polar, polar amino acid residue, residue at position X177 is an aliphatic amino acid residue, residue at position X211 is an basic amino acid residue, residue at position X294 is a non-polar or aliphatic amino acid residue, residue at position X324 is a non-polar amino acid residue, and residue at position X391 is an aliphatic amino acid residue.

In some embodiments, the amino acid residue at the residue positions is selected from the following: residue at position X9 is T, residue at position X45 is H, residue at position X86 is Y, residue at position X177 is L, residue at position X211 is K, residue at position X294 is V, residue at position X324 is G, and residue at position X391 is A.

In some embodiments, the transaminase polypeptide having increased enzymatic activity and increased thermo/solvent stability in the conversion of 3′-hydroxyacetophenone to the product (S)-3-(1-aminoethyl)-phenol comprises an amino acid sequence selected from SEQ ID NO: 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, and 44.

Structure and function information for exemplary non-naturally occurring (or engineered) transaminase polypeptides of the present disclosure are shown below in Table 2. The odd numbered sequence identifiers (i.e., SEQ ID NOs) refer to the nucleotide sequence encoding the amino acid sequence provided by the even numbered SEQ ID NOs, and the sequences are provided in the electronic sequence listing file accompanying this disclosure, which is hereby incorporated by reference herein. The amino acid residue differences are based on comparison to the reference sequence of SEQ ID NO: 2, which is a naturally occurring wild-type transaminase of Vibrio fluvialis. The activity of each engineered polypeptide relative to the reference polypeptide of SEQ ID NO: 2 was determined as conversion of the 3′-hydroxyacetophenone substrate of compound (1) to the (S)-3-(1-aminoethyl)-phenol product of compound (2) over a set time period and temperature in a high-throughput (HTP) assay (used as the primary screen) as well as shake-flask powder (SFP) and downstream process powder (DSP) assays (used as secondary screens for many of the engineered polypeptides). SFP and DSP preparations include approximately 30% and approximately 80% total protein, respectively, and thus, provide more purified enzyme preparations compared to the cell lysate used in HTP assays.

The HTP Assay Activity is determined using E. coli cell lysate under the following general reaction conditions: 200 μL total volume, 40 μL cell lysate, 1.5 M IPM, 1 mM PLP, 34 g/L substrate of compound (1), 100 mM TEA-HCl, 5% (v/v) DMSO, pH 7.5, and 24 h reaction time. Further modifications to the HTP assay made for improved screening of engineered polypeptides are described in Example 1. The SFP Assay Activity and DSP Assay Activity is determined using SFP and DSP preparations of the engineered polypeptides and the following general conditions: 27 g/L 3-hydroxyacetophenone substrate, 20 g/L transaminase SFP or DSP powder, 1.5 M IPM-HCl, 1 mM PLP, 0.1 mM TEA-HCl buffer, pH 7.5, allowed to react at ambient temperature for 24-48 hours. Further modifications to the SFP and DSP assay made for improved screening of engineered polypeptides are described in Example 1.

The levels of activity (i.e., “+” “++” “+++” etc.) are defined as follows: “+” indicates at least equal to but less than 2 times the activity of SEQ ID NO: 2; “++” indicates at least 2 times but less than 5 times the activity of SEQ ID NO: 2; “+++” indicates at least 5 times but less than 10 times the activity of SEQ ID NO: 2; “++++” indicates at least 10 times but less than 25 times the activity of SEQ ID NO: 2; “+++++” indicates at least 25 times but less than 50 times the activity of SEQ ID NO: 2; “++++++” indicates at least 50 times or greater than the activity of SEQ ID NO: 2.

TABLE 2 Engineered Polypeptides and Relative Activity Improvements # of HTP SFP DSP Residue Assay Assay Assay Differences Activity Activity Activity SEQ ID (relative to (relative to (relative to (relative to NO: Amino Acid Residue Differences SEQ ID SEQ ID SEQ ID SEQ ID (nt/aa) (relative to SEQ ID NO: 2) NO: 2) NO: 2) NO: 2) NO: 2) 3/4 A9T; N45H; F86Y; V177L; R211K; 8 ++++ n.d. + M294V; S324G; T391A; 5/6 A9T; N45H; F86Y; V153S; V177L; 10 ++++ n.d. + R211K; P233S; M294V; S324G; T391A; 7/8 A9T; N45H; F86Y; V153S; V177L; 10 ++++++ ++ ++ R211K; P233I; M294V; S324G; T391A;  9/10 A9T; N45H; F86Y; V153S; K163F; 11 ++++++ ++ +++ V177L; R211K; P233I; M294V; S324G; T391A; 11/12 A9T; N45H; F86Y; V153S; K163F; 14 ++++++ +++ +++ V177L; R211K; P233I; A235P; M294V; S324G; T391A; C424A; F427Y; 13/14 A9T; G18A; N45H; F86Y; V153S; 18 ++++++ +++ +++ K163F; V177L; R211K; P233I; A235P; N286S; M294V; A323T; S324G; A383V; T391A; C424A; F427Y; 15/16 A9T; N45H; F86Y; V153S; K163F; 17 ++++++ +++ +++ S167K; V168D; P174E; V177L; R211K; P233I; A235P; M294V; S324G; T391A; C424A; F427Y; 17/18 A9T; G18A; D21H; N45H; F86Y; 19 ++++++ +++ ++++ V153S; K163F; V177L; R211K; P233I; A235P; N286S; M294V; A323T; S324G; A383V; T391A; C424A; F427Y; 19/20 A9T; G18A; D21H; N45H; F86Y; 19 ++++++ +++ n.d. W147K; V153S; K163F; V177L; R211K; P233T; A235P; M294V; A323T; S324G; A383V; T391A; C424A; F427Y; 21/22 A9T; G18A; D21H; N45H; F86Y; 20 ++++++ ++++ n.d. W147K; V153S; K163F; V177L; R211K; P233I; A235P; P244T; M294V; A323T; S324G; A383V; T391A; C424A; F427Y; 23/24 A9T; G18A; D21H; N45H; F86Y; 20 ++++++ ++++ n.d. W147K; V153S; K163F; V177L; R211K; P233T; A235P; P244T; M294V; A323T; S324G; A383V; T391A; C424A; F427Y; 25/26 A9T; G18A; D21H; N45H; F86Y; 19 n.d. ++++ n.d. V153S; K163F; V177L; R211K; P233I; A235P; N286S; M294V; A323T; S324G; A383V; T391A; C424A; F427Y; 27/28 A9T; G18A; D21H; N45H; F86Y; 20 n.d. n.d. ++++ W147K; V153S; K163F; V177L; R211K; P233I; A235P; P244T; M294V; A323T; S324G; A383V; T391A; C424A; F427Y; 29/30 A9T; G18A; D21H; N45H; F86Y; 24 ++++++ ++++ n.d. F130L; A133R; R146L; W147K; V153S; K163F; P164S; V177L; R211K; P233T; A235P; P244T; M294V; A323T; S324G; A383V; T391A; C424A; F427Y; 31/32 A9T; G18A; D21H; V31M; N45H; 23 ++++++ +++ +++++ F86Y; A133R; R146L; W147K; V153S; K163F; V177L; R211K; P233T; A235P; P244T; M294V; A323T; S324G; A383V; T391A; C424A; F427Y; 33/34 A9T; G18A; D21H; N45H; F86Y; 21 ++++++ +++ n.d. F130L; W147K; V153S; K163F; V177L; P233I; A235P; P244T; M294V; E316H; A323T; S324G; A383V; T391A; C424A; F427Y; 35/36 A9T; G18A; D21H; V31M; N45H; 24 ++++++ ++++ +++++ F86Y; A133R; R146L; W147K; V153S; K163F; V177L; R211K; P233T; A235P; P244T; M294V; P318D; A323T; S324G; A383V; T391A; C424A; F427Y; 37/38 A9T; G18A; D21H; V31M; N45H; 29 ++++++ +++++ n.d. F86Y; Y113V; D122E; A133R; R146L; W147K; V153S; K163F; P164G; V177L; R211K; P233T; A235P; P244T; P293S; M294V; P318D; A323T; S324G; I375V; A383V; T391A; C424A; F427Y; 39/40 A9T; G18A; D21H; V31M; N45H; 29 ++++++ +++++ +++++ F86Y; Y113V; D122E; A133R; R146L; W147K; V153S; K163H; P164G; V168K; V177L; R211K; P233T; A235P; P244T; M294V; P318D; A323T; S324G; I375V; A383V; T391A; C424A; F427Y; 41/42 A9T; G18A; D21H; V31M; N45H; 25 ++++++ ++++ n.d. F86Y; F130M; A133R; R146L; W147K; V153S; K163F; V177L; R211K; P233T; A235P; P244T; M294V; P318D; A323T; S324G; A383V; T391A; C424A; F427Y; 43/44 A9T; G18A; D21H; V31M; N45H; 31 ++++++ ++++++ +++++ F86Y; Y113V; D122E; A133R; R146L; W147K; V153S; K163H; P164G; V168K; V177L; R211K; P233T; A235P; P244T; M294V; P318D; A323T; S324G; I332T; I375V; A383V; T391A; G418Q; C424A; F427Y;

In some embodiments, the engineered transaminase polypeptides of the present disclosure which are capable of converting compound (1) to compound (2) comprise an amino acid sequence selected from any one of SEQ ID NO: 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, and 44. As shown above in Table 2, each of these polypeptides comprises one or more amino acid residue differences as compared to SEQ ID NO: 2, and has at least 2-fold, at least 5-fold, at least 10-fold, at least 25-fold, or at least 50-fold increased activity relative to the activity of the reference polypeptide of SEQ ID NO: 2. Specific amino acid differences are shown in Table 2 and include one or more residue differences as compared to SEQ ID NO:2 at the following residue positions: X18, X21, X31, X113, X122, X130, X133, X146, X147, X153, X163, X164, X167, X168, X174, X233; X235, X244, X286; X293, X316, X318; X323, X332, X375, X383, X418, X424, and X427.

In some embodiments, the present disclosure provides an engineered polypeptide capable of converting compound (1) to compound (2) with at least 2-fold, at least 5-fold, at least 10-fold, at least 25-fold, or at least 50-fold increased activity relative to the activity of the polypeptide of SEQ ID NO: 2, and comprises an amino acid sequence having at least 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to a reference amino acid sequence selected from any one of SEQ ID NO: 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, and 44.

In some embodiments, the present disclosure provides a non-naturally occurring polypeptide capable of converting compound (1) to compound (2) with at least 2-fold, at least 5-fold, at least 10-fold, at least 25-fold, or at least 50-fold increased activity relative to the activity of the polypeptide of SEQ ID NO: 2, comprises an amino acid sequence having at least 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to SEQ ID NO: 2, and further comprises a set of amino acid residue differences as compared to SEQ ID NO:2 of any one of SEQ ID NO: 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, or 44. In some embodiments, in addition to the set of amino acid residue differences of any one of the non-naturally occurring polypeptides of SEQ ID NO: 8 through SEQ ID NO: 44, the sequence of the non-naturally occurring polypeptide can further comprise 1-2,1-3, 1-4,1-5, 1-6,1-7, 1-8,1-9, 1-10, 1-11, 1-12, 1-14, 1-15, 1-16, 1-18, 1-20, 1-22, 1-24, 1-26, 1-30, 1-35, 1-40 residue differences at other amino acid residue positions as compared to the SEQ ID NO: 2. In some embodiments, the residue differences can comprise conservative substitutions and non-conservative substitutions as compared to SEQ ID NO: 2.

In some embodiments, a transaminase polypeptide comprises an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO:2 or SEQ ID NO:4, wherein the amino acid sequence comprises any one of the set of mutations contained in any one of the sequences listed in Table 2 as compared to a reference sequence corresponding to SEQ ID NO:2. In some embodiments, the engineered transaminases can have additionally about 1-2,1-3, 1-4,1-5, 1-6,1-7, 1-8,1-9, 1-10, 1-15, 1-20, 1-21, 1-22, 1-23, 1-24, 1-25, 1-30, 1-35, 1-40, 1-45, 1-50, 1-55, or 1-60 residue differences at other residue positions. In some embodiments, the number of differences as compared to the reference sequence can be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 30, 35, 40, 45, 50, 55, or 60 residue positions. In some embodiments, the residue differences comprise conservative mutations.

In some embodiments, a transaminase polypeptide comprises an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to a reference sequence selected from SEQ ID NO: 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, and 44, wherein the engineered transaminase amino acid sequence comprises any one of the set of mutations contained in any one of the sequences listed in Table 2 as compared to a reference sequence corresponding to SEQ ID NO:2. In some embodiments, these engineered transaminases can have additionally about 1-2,1-3, 1-4,1-5, 1-6,1-7, 1-8,1-9, 1-10, 1-15, 1-20, 1-21, 1-22, 1-23, 1-24, 1-25, 1-30, 1-35, 1-40, 1-45, 1-50, 1-55, or 1-60 residue differences at other residue positions. In some embodiments, the number of differences as compared to the reference sequence can be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 30, 35, 40, 45, 50, 55, or 60 residue positions. In some embodiments, the residue differences comprise conservative mutations.

In some embodiments, the transaminase polypeptide comprises an amino acid sequence that includes the following: residue at position X9 is a polar amino acid residue particularly T; residue at position X45 is a constrained amino acid residue, particularly H; residue at position X86 is a cysteine, or an aliphatic, non-polar, or polar amino acid residue, particularly Y; residue at position X153 is a polar amino acid residue, particularly S; residue at position X177 is an aliphatic amino acid residue, particularly L; residue at position X211 is a basic amino acid residue, particularly K; residue at position X233 is an aliphatic or polar amino acid residue, particularly I; residue at position X294 is a non-polar or aliphatic amino acid residue, particularly V; residue at position X324 is a non-polar amino acid residue, particularly G; and residue at position X391 is an aliphatic amino acid residue, particularly A. In some embodiments, the transaminase polypeptides can have additionally 1-2,1-3, 1-4,1-5, 1-6,1-7, 1-8,1-9, 1-10, 1-11, 1-12, 1-14, 1-15, 1-16, 1-18, 1-20, 1-22, 1-24, 1-26, 1-30, 1-35, 1-40, 1-45, 1-50, 1-55, or 1-60 residue differences at other residue positions. In some embodiments, the number of differences can be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 18, 20, 22, 24, 26, 30, 35, 40, 45, 50, 55, or 60 residue differences at the other residue positions. In some embodiments, the engineered transaminase polypeptide can comprise an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% identical to a reference sequence based on SEQ ID NO:2 or SEQ ID NO:4 having the features described for preceding specified residue positions (e.g., SEQ ID NO:8), with the proviso that the engineered transaminase polypeptide comprises an amino acid sequence that includes at least the features described for the specified residue positions. In some embodiments, the engineered transaminase polypeptide can comprise an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% identical to a reference sequence of SEQ ID NO:8.

In some embodiments, the transaminase polypeptide comprises an amino acid sequence that includes the following: residue at position X9 is a polar amino acid residue particularly T; residue at position X45 is a constrained amino acid residue, particularly H; residue at position X86 is a cysteine, or an aliphatic, non-polar, or polar amino acid residue, particularly Y; residue at position X153 is a polar amino acid residue, particularly S; residue at position X163 is a constrained or aromatic amino acid residue, particularly F; residue at position X177 is an aliphatic amino acid residue, particularly L; residue at position X211 is a basic amino acid residue, particularly K; residue at position X233 is an aliphatic or polar amino acid residue, particularly I; residue at position X294 is a non-polar or aliphatic amino acid residue, particularly V; residue at position X324 is a non-polar amino acid residue, particularly G; and residue at position X391 is an aliphatic amino acid residue, particularly A. In some embodiments, the transaminase polypeptides can have additionally 1-2,1-3, 1-4,1-5, 1-6,1-7, 1-8,1-9, 1-10, 1-11, 1-12, 1-14, 1-15, 1-16, 1-18, 1-20, 1-22, 1-24, 1-26, 1-30, 1-35, 1-40, 1-45, 1-50, 1-55, or 1-60 residue differences at other residue positions. In some embodiments, the number of differences can be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 18, 20, 22, 24, 26, 30, 35, 40, 45, 50, 55, or 60 residue differences at the other residue positions. In some embodiments, the engineered transaminase polypeptide can comprise an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% identical to a reference sequence based on SEQ ID NO:2 or SEQ ID NO:4 having the features described for preceding specified residue positions (e.g., SEQ ID NO:10), with the proviso that the engineered transaminase polypeptide comprises an amino acid sequence that includes at least the features described for the specified residue positions. In some embodiments, the engineered transaminase polypeptide can comprise an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% identical to a reference sequence of SEQ ID NO:10.

In some embodiments, the transaminase polypeptide comprises an amino acid sequence that includes the following: residue at position X9 is a polar amino acid residue particularly T; residue at position X18 is an aliphatic amino acid residue, particularly A; residue at position X45 is a constrained amino acid residue, particularly H; residue at position X86 is a cysteine, or an aliphatic, non-polar, or polar amino acid residue, particularly Y; residue at position X153 is a polar amino acid residue, particularly S; residue at position X163 is a constrained or aromatic amino acid residue, particularly F; residue at position X177 is an aliphatic amino acid residue, particularly L; residue at position X211 is a basic amino acid residue, particularly K; residue at position X233 is an aliphatic or polar amino acid residue, particularly T; residue at position X235 is a constrained amino acid residue, particularly P; residue at position X294 is a non-polar or aliphatic amino acid residue, particularly V; residue at position X323 is a polar amino acid residue, particularly T; residue at position X324 is a non-polar amino acid residue, particularly G; residue at position X383 is an aliphatic amino acid residue, particularly V; residue at position X391 is an aliphatic amino acid residue, particularly A; residue at position X424 is an aliphatic amino acid residue, particularly A; and residue at position X427 is an aromatic amino acid residue, particularly Y. In some embodiments, the transaminase polypeptides can have additionally 1-2,1-3, 1-4,1-5, 1-6,1-7, 1-8,1-9, 1-10, 1-11, 1-12, 1-14, 1-15, 1-16, 1-18, 1-20, 1-22, 1-24, 1-26, 1-30, 1-35, 1-40, 1-45, 1-50, 1-55, or 1-60 residue differences at other residue positions. In some embodiments, the number of differences can be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 18, 20, 22, 24, 26, 30, 35, 40, 45, 50, 55, or 60 residue differences at the other residue positions. In some embodiments, the engineered transaminase polypeptide can comprise an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% identical to a reference sequence based on SEQ ID NO:2 or SEQ ID NO:4 having the features described for preceding specified residue positions (e.g., SEQ ID NO:14), with the proviso that the engineered transaminase polypeptide comprises an amino acid sequence that includes at least the features described for the specified residue positions. In some embodiments, the engineered transaminase polypeptide can comprise an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% identical to a reference sequence of SEQ ID NO: 14.

In some embodiments, the transaminase polypeptide comprises an amino acid sequence that includes the following: residue at position X9 is a polar amino acid residue particularly T; residue at position X18 is an aliphatic amino acid residue, particularly A; residue at position X21 is a constrained amino acid residue, particularly H; residue at position X45 is a constrained amino acid residue, particularly H; residue at position X86 is a cysteine, or an aliphatic, non-polar, or polar amino acid residue, particularly Y; residue at position X153 is a polar amino acid residue, particularly S; residue at position X163 is a constrained or aromatic amino acid residue, particularly F; residue at position X177 is an aliphatic amino acid residue, particularly L; residue at position X211 is a basic amino acid residue, particularly K; residue at position X233 is an aliphatic or polar amino acid residue, particularly T; residue at position X235 is a constrained amino acid residue, particularly P; residue at position X294 is a non-polar or aliphatic amino acid residue, particularly V; residue at position X323 is a polar amino acid residue, particularly T; residue at position X324 is a non-polar amino acid residue, particularly G; residue at position X383 is an aliphatic amino acid residue, particularly V; residue at position X391 is an aliphatic amino acid residue, particularly A; residue at position X424 is an aliphatic amino acid residue, particularly A; and residue at position X427 is an aromatic amino acid residue, particularly Y. In some embodiments, the transaminase polypeptides can have additionally 1-2,1-3, 1-4,1-5, 1-6,1-7, 1-8,1-9, 1-10, 1-11, 1-12, 1-14, 1-15, 1-16, 1-18, 1-20, 1-22, 1-24, 1-26, 1-30, 1-35, 1-40, 1-45, 1-50, 1-55, or 1-60 residue differences at other residue positions. In some embodiments, the number of differences can be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 18, 20, 22, 24, 26, 30, 35, 40, 45, 50, 55, or 60 residue differences at the other residue positions. In some embodiments, the engineered transaminase polypeptide can comprise an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% identical to a reference sequence based on SEQ ID NO:2 or SEQ ID NO:4 having the features described for preceding specified residue positions (e.g., SEQ ID NO:18), with the proviso that the engineered transaminase polypeptide comprises an amino acid sequence that includes at least the features described for the specified residue positions. In some embodiments, the engineered transaminase polypeptide can comprise an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% identical to a reference sequence of SEQ ID NO:18.

In some embodiments, the transaminase polypeptide comprises an amino acid sequence that includes the following: residue at position X9 is a polar amino acid residue particularly T; residue at position X18 is an aliphatic amino acid residue, particularly A; residue at position X21 is a constrained amino acid residue, particularly H; residue at position X45 is a constrained amino acid residue, particularly H; residue at position X86 is a cysteine, or an aliphatic, non-polar, or polar amino acid residue, particularly Y; residue at position X147 is a basic amino acid residue, particularly K; residue at position X153 is a polar amino acid residue, particularly S; residue at position X163 is a constrained or aromatic amino acid residue, particularly F; residue at position X177 is an aliphatic amino acid residue, particularly L; residue at position X211 is a basic amino acid residue, particularly K; residue at position X233 is an aliphatic or polar amino acid residue, particularly T; residue at position X235 is a constrained amino acid residue, particularly P; residue at position X244 is a polar amino acid residue, particularly T; residue at position X294 is a non-polar or aliphatic amino acid residue, particularly V; residue at position X323 is a polar amino acid residue, particularly T; residue at position X324 is a non-polar amino acid residue, particularly G; residue at position X383 is an aliphatic amino acid residue, particularly V; residue at position X391 is an aliphatic amino acid residue, particularly A; residue at position X424 is an aliphatic amino acid residue, particularly A; and residue at position X427 is an aromatic amino acid residue, particularly Y. In some embodiments, the transaminase polypeptides can have additionally 1-2,1-3, 1-4,1-5, 1-6,1-7, 1-8,1-9, 1-10, 1-11, 1-12, 1-14, 1-15, 1-16, 1-18, 1-20, 1-22, 1-24, 1-26, 1-30, 1-35, 1-40, 1-45, 1-50, 1-55, or 1-60 residue differences at other residue positions. In some embodiments, the number of differences can be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 18, 20, 22, 24, 26, 30, 35, 40, 45, 50, 55, or 60 residue differences at the other residue positions. In some embodiments, the engineered transaminase polypeptide can comprise an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% identical to a reference sequence based on SEQ ID NO:2 or SEQ ID NO:4 having the features described for preceding specified residue positions (e.g., SEQ ID NO:28), with the proviso that the engineered transaminase polypeptide comprises an amino acid sequence that includes at least the features described for the specified residue positions. In some embodiments, the engineered transaminase polypeptide can comprise an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% identical to a reference sequence of SEQ ID NO:28.

In some embodiments, the transaminase polypeptide comprises an amino acid sequence that includes the following: residue at position X9 is a polar amino acid residue particularly T; residue at position X18 is an aliphatic amino acid residue, particularly A; residue at position X21 is a constrained amino acid residue, particularly H; residue at position X31 is a non-polar amino acid residue, particularly M; residue at position X45 is a constrained amino acid residue, particularly H; residue at position X86 is a cysteine, or an aliphatic, non-polar, or polar amino acid residue, particularly Y; residue at position X133 is a basic amino acid residue, particularly R; residue at position X146 is an aliphatic amino acid residue, particularly L; residue at position X147 is a basic amino acid residue, particularly K; residue at position X153 is a polar amino acid residue, particularly S; residue at position X163 is a constrained or aromatic amino acid residue, particularly F; residue at position X177 is an aliphatic amino acid residue, particularly L; residue at position X211 is a basic amino acid residue, particularly K; residue at position X233 is an aliphatic or polar amino acid residue, particularly T; residue at position X235 is a constrained amino acid residue, particularly P; residue at position X244 is a polar amino acid residue, particularly T; residue at position X294 is a non-polar or aliphatic amino acid residue, particularly V; residue at position X323 is a polar amino acid residue, particularly T; residue at position X324 is a non-polar amino acid residue, particularly G; residue at position X383 is an aliphatic amino acid residue, particularly V; residue at position X391 is an aliphatic amino acid residue, particularly A; residue at position X424 is an aliphatic amino acid residue, particularly A; residue at position X427 is an aromatic amino acid residue, particularly Y. In some embodiments, the transaminase polypeptides can have additionally 1-2,1-3, 1-4,1-5, 1-6,1-7, 1-8,1-9, 1-10, 1-11, 1-12, 1-14, 1-15, 1-16, 1-18, 1-20, 1-22, 1-24, 1-26, 1-30, 1-35, 1-40, 1-45, 1-50, 1-55, or 1-60 residue differences at other residue positions. In some embodiments, the number of differences can be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 18, 20, 22, 24, 26, 30, 35, 40, 45, 50, 55, or 60 residue differences at the other residue positions. In some embodiments, the engineered transaminase polypeptide can comprise an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% identical to a reference sequence based on SEQ ID NO:2 or SEQ ID NO:4 having the features described for preceding specified residue positions (e.g., SEQ ID NO:32), with the proviso that the engineered transaminase polypeptide comprises an amino acid sequence that includes at least the features described for the specified residue positions. In some embodiments, the engineered transaminase polypeptide can comprise an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% identical to a reference sequence of SEQ ID NO:32.

In some embodiments, the transaminase polypeptide comprises an amino acid sequence that includes the following: residue at position X9 is a polar amino acid residue particularly T; residue at position X18 is an aliphatic amino acid residue, particularly A; residue at position X21 is a constrained amino acid residue, particularly H; residue at position X31 is a non-polar amino acid residue, particularly M; residue at position X45 is a constrained amino acid residue, particularly H; residue at position X86 is a cysteine, or an aliphatic, non-polar, or polar amino acid residue, particularly Y; residue at position X113 is an aliphatic amino acid residue, particularly V; residue at position X122 is an acidic amino acid residue, particularly E; residue at position X133 is a basic amino acid residue, particularly R; residue at position X146 is an aliphatic amino acid residue, particularly L; residue at position X147 is a basic amino acid residue, particularly K; residue at position X153 is a polar amino acid residue, particularly S; residue at position X163 is a constrained or aromatic amino acid residue, particularly H; residue at position X164 is a polar or non-polar amino acid residue, particularly G; residue at position X168 is a basic or acidic amino acid residue, particularly K; residue at position X177 is an aliphatic amino acid residue, particularly L; residue at position X211 is a basic amino acid residue, particularly K; residue at position X233 is an aliphatic or polar amino acid residue, particularly T; residue at position X235 is a constrained amino acid residue, particularly P; residue at position X244 is a polar amino acid residue, particularly T; residue at position X294 is a non-polar or aliphatic amino acid residue, particularly V; residue at position X318 is an acidic amino acid residue, particularly D; residue at position X323 is a polar amino acid residue, particularly T; residue at position X324 is a non-polar amino acid residue, particularly G; residue at position X383 is an aliphatic amino acid residue, particularly V; residue at position X391 is an aliphatic amino acid residue, particularly A; residue at position X424 is an aliphatic amino acid residue, particularly A; residue at position X427 is an aromatic amino acid residue, particularly Y. In some embodiments, the transaminase polypeptides can have additionally 1-2,1-3, 1-4,1-5, 1-6,1-7, 1-8,1-9, 1-10, 1-11, 1-12, 1-14, 1-15, 1-16, 1-18, 1-20, 1-22, 1-24, 1-26, 1-30, 1-35, 1-40, 1-45, 1-50, 1-55, or 1-60 residue differences at other residue positions. In some embodiments, the number of differences can be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 18, 20, 22, 24, 26, 30, 35, 40, 45, 50, 55, or 60 residue differences at the other residue positions. In some embodiments, the engineered transaminase polypeptide can comprise an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% identical to a reference sequence based on SEQ ID NO:2 or SEQ ID NO:4 having the features described for preceding specified residue positions (e.g., SEQ ID NO:36), with the proviso that the engineered transaminase polypeptide comprises an amino acid sequence that includes at least the features described for the specified residue positions. In some embodiments, the engineered transaminase polypeptide can comprise an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% identical to a reference sequence of SEQ ID NO:36.

In some embodiments, the transaminase polypeptide comprises an amino acid sequence that includes the following: residue at position X9 is a polar amino acid residue particularly T; residue at position X18 is an aliphatic amino acid residue, particularly A; residue at position X21 is a constrained amino acid residue, particularly H; residue at position X31 is a non-polar amino acid residue, particularly M; residue at position X45 is a constrained amino acid residue, particularly H; residue at position X86 is a cysteine, or an aliphatic, non-polar, or polar amino acid residue, particularly Y; residue at position X113 is an aliphatic amino acid residue, particularly V; residue at position X122 is an acidic amino acid residue, particularly E; residue at position X133 is a basic amino acid residue, particularly R; residue at position X146 is an aliphatic amino acid residue, particularly L; residue at position X147 is a basic amino acid residue, particularly K; residue at position X153 is a polar amino acid residue, particularly S; residue at position X163 is a constrained or aromatic amino acid residue, particularly H; residue at position X164 is a polar or non-polar amino acid residue, particularly G; residue at position X168 is a basic or acidic amino acid residue, particularly K; residue at position X177 is an aliphatic amino acid residue, particularly L; residue at position X211 is a basic amino acid residue, particularly K; residue at position X233 is an aliphatic or polar amino acid residue, particularly T; residue at position X235 is a constrained amino acid residue, particularly P; residue at position X244 is a polar amino acid residue, particularly T; residue at position X294 is a non-polar or aliphatic amino acid residue, particularly V; residue at position X318 is an acidic amino acid residue, particularly D; residue at position X323 is a polar amino acid residue, particularly T; residue at position X324 is a non-polar amino acid residue, particularly G; residue at position X375 is an aliphatic amino acid residue, particularly V; residue at position X383 is an aliphatic amino acid residue, particularly V; residue at position X391 is an aliphatic amino acid residue, particularly A; residue at position X424 is an aliphatic amino acid residue, particularly A; residue at position X427 is an aromatic amino acid residue, particularly Y. In some embodiments, the transaminase polypeptides can have additionally 1-2,1-3, 1-4,1-5, 1-6,1-7, 1-8,1-9, 1-10, 1-11, 1-12, 1-14, 1-15, 1-16, 1-18, 1-20, 1-22, 1-24, 1-26, 1-30, 1-35, 1-40, 1-45, 1-50, 1-55, or 1-60 residue differences at other residue positions. In some embodiments, the number of differences can be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 18, 20, 22, 24, 26, 30, 35, 40, 45, 50, 55, or 60 residue differences at the other residue positions. In some embodiments, the engineered transaminase polypeptide can comprise an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% identical to a reference sequence based on SEQ ID NO:2 or SEQ ID NO:4 having the features described for preceding specified residue positions (e.g., SEQ ID NO:40), with the proviso that the engineered transaminase polypeptide comprises an amino acid sequence that includes at least the features described for the specified residue positions. In some embodiments, the engineered transaminase polypeptide can comprise an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% identical to a reference sequence of SEQ ID NO:40.

In some embodiments, the engineered transaminase polypeptide comprises a deletion of the engineered transaminase polypeptides described herein. Thus, for each and every embodiment of the transaminase polypeptides of the disclosure, the deletions can comprise one or more amino acids, 2 or more amino acids, 3 or more amino acids, 4 or more amino acids, 5 or more amino acids, 6 or more amino acids, 8 or more amino acids, 10 or more amino acids, 15 or more amino acids, or 20 or more amino acids, up to 10% of the total number of amino acids, up to 10% of the total number of amino acids, up to 20% of the total number of amino acids, or up to 30% of the total number of amino acids of the transaminase polypeptides, where the functional activity and/or improved properties of the transaminase described herein is maintained. In some embodiments, the deletions can comprise, 1-2, 1-3,1-4, 1-5,1-6, 1-7,1-8, 1-9,1-10, 1-15, 1-20, 1-21, 1-22, 1-23, 1-24, 1-25, 1-30, 1-35, 1-40, 1-45, 1-50, 1-55, or 1-60 amino acid residues. In some embodiments, the number of deletions can be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 30, 35, 40, 45, 50, 55, or 60 amino acids. In some embodiments, the deletions can comprise deletions of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 20, 21, 22, 23, 24, 25 or 30 amino acid residues.

In some embodiments, the improved engineered transaminase polypeptides can comprise fragments of the engineered transaminase enzymes described herein. In some embodiments, the polypeptide fragments can be 80%, 90%, 95%, 98%, or 99% of the full-length transaminase polypeptide, such as the transaminase of SEQ ID NO: 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, and 44, where the functional activity and/or improved properties of the transaminase described herein is maintained.

In some embodiments, the transaminase polypeptide can have an insertion or one or more amino acids to a sequence of an engineered transaminase described herein. Thus, for each and every embodiment of the transaminase polypeptides of the disclosure, the insertions can comprise one or more amino acids, 2 or more amino acids, 3 or more amino acids, 4 or more amino acids, 5 or more amino acids, 6 or more amino acids, 8 or more amino acids, 10 or more amino acids, 15 or more amino acids, or 20 or more amino acids, where the functional activity and/or improved properties of the transaminase described herein is maintained. The insertions can be to amino or carboxy terminus of the transaminase, or internal portions of the transaminase polypeptide.

In addition to the residue positions specified above, any of the engineered transaminase polypeptides disclosed herein can further comprise other residue differences relative to SEQ ID NO:2 at other residue positions. Residue differences at these other residue positions provide for additional variations in the amino acid sequence without adversely affecting the ability of the polypeptide to carry out the conversion of compound (1) to compound (2). In some embodiments, the polypeptides can have additionally 1-2,1-3, 1-4,1-5, 1-6,1-7, 1-8,1-9, 1-10,1-11,1-12,1-14,1-15,1-16,1-18,1-20, 1-22, 1-24, 1-26, 1-30, 1-35, 1-40 residue differences at other amino acid residue positions as compared to the reference sequence. In some embodiments, the number of differences can be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 18, 20, 22, 24, 26, 30, 35, and 40 residue differences at other residue positions. The residue difference at these other positions can include conservative changes or non-conservative changes. In some embodiments, the residue differences can comprise conservative substitutions and non-conservative substitutions as compared to the wild-type transaminase polypeptide of SEQ ID NO: 2.

Amino acid residue differences at other positions relative to the wild-type sequence of SEQ ID NO: 2 and the affect of these differences on enzyme function are provide by other engineered transaminase polypeptides disclosed in U.S. application Ser. No. 12/684,864, filed Jan. 8, 2010, which is hereby incorporated by reference herein. Accordingly, in some embodiments, one or more of the amino acid differences provided in the engineered transaminase polypeptides of U.S. application Ser. No. 12/684,864, filed Jan. 8, 2010, could also be introduced into a engineered transaminase polypeptide of the present disclosure.

In some embodiments, the present disclosure provides a non-naturally occurring polypeptide capable of converting compound (1) to compound (2) with at least 2-fold, at least 2-fold, at least 5-fold, at least 10-fold, at least 25-fold, or at least 50-fold increased activity relative to the activity of the polypeptide of SEQ ID NO: 2, which comprises an amino acid sequence having at least 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to SEQ ID NO: 2, with the proviso that the amino acid sequence of any one or more of the engineered transaminase polypeptides disclosed in U.S. application Ser. No. 12/684,864, filed Jan. 8, 2010.

In some embodiments, the polypeptides of the disclosure can be in the form of fusion polypeptides in which the engineered polypeptides are fused to other polypeptides, such as, by way of example and not limitation, antibody tags (e.g., myc epitope), purification sequences (e.g., His tags for binding to metals), and cell localization signals (e.g., secretion signals). Thus, the engineered polypeptides described herein can be used with or without fusions to other polypeptides.

The polypeptides described herein are not restricted to the genetically encoded amino acids. In addition to the genetically encoded amino acids, the polypeptides described herein may be comprised, either in whole or in part, of naturally-occurring and/or synthetic non-encoded amino acids. Certain commonly encountered non-encoded amino acids of which the polypeptides described herein may be comprised include, but are not limited to: the D-stereomers of the genetically-encoded amino acids; 2,3-diaminopropionic acid (Dpr); α-aminoisobutyric acid (Aib); g-aminohexanoic acid (Aha); δ-aminovaleric acid (Ava); N-methylglycine or sarcosine (MeGly or Sar); ornithine (Orn); citrulline (Cit); t-butylalanine (Bua); t-butylglycine (Bug); N-methylisoleucine (MeIle); phenylglycine (Phg); cyclohexylalanine (Cha); norleucine (Nle); naphthylalanine (NaI); 2-chlorophenylalanine (Ocf); 3-chlorophenylalanine (Mcf); 4-chlorophenylalanine (Pcf); 2-fluorophenylalanine (Off); 3-fluorophenylalanine (Mff); 4-fluorophenylalanine (Pff); 2-bromophenylalanine (Obf); 3-bromophenylalanine (Mbf); 4-bromophenylalanine (Pbf); 2-methylphenylalanine (Omf); 3-methylphenylalanine (Mmf); 4-methylphenylalanine (Pmf); 2-nitrophenylalanine (Onf); 3-nitrophenylalanine (Mnf); 4-nitrophenylalanine (Pnf); 2-cyanophenylalanine (Ocf); 3-cyanophenylalanine (Mcf); 4-cyanophenylalanine (Pcf); 2-trifluoromethylphenylalanine (Off); 3-trifluoromethylphenylalanine (Mtf); 4-trifluoromethylphenylalanine (Ptf); 4-aminophenylalanine (Paf); 4-iodophenylalanine (Pif); 4-aminomethylphenylalanine (Pamf); 2,4-dichlorophenylalanine (Opef); 3,4-dichlorophenylalanine (Mpcf); 2,4-difluorophenylalanine (Opff); 3,4-difluorophenylalanine (Mpff); pyrid-2-ylalanine (2pAla); pyrid-3-ylalanine (3pAla); pyrid-4-ylalanine (4pAla); naphth-1-ylalanine (1nAla); naphth-2-ylalanine (2nAla); thiazolylalanine (taAla); benzothienylalanine (bAla); thienylalanine (tAla); furylalanine (fAla); homophenylalanine (hPhe); homotyrosine (hTyr); homotryptophan (hTrp); pentafluorophenylalanine (5ff); styrylkalanine (sAla); authrylalanine (aAla); 3,3-diphenylalanine (Dfa); 3-amino-5-phenypentanoic acid (Afp); penicillamine (Pen); 1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid (Tic); β-2-thienylalanine (Thi); methionine sulfoxide (Mso); N(w)-nitroarginine (nArg); homolysine (hLys); phosphonomethylphenylalanine (pmPhe); phosphoserine (pSer); phosphothreonine (pThr); homoaspartic acid (hAsp); homoglutanic acid (hGlu); 1-aminocyclopent-(2 or 3)-ene-4 carboxylic acid; pipecolic acid (PA), azetidine-3-carboxylic acid (ACA); 1-aminocyclopentane-3-carboxylic acid; allylglycine (aOly); propargylglycine (pgGly); homoalanine (hAla); norvaline (nVal); homoleucine (hLeu), homovaline (hVal); homoisolencine (hIle); homoarginine (hArg); N-acetyl lysine (AcLys); 2,4-diaminobutyric acid (Dbu); 2,3-diaminobutyric acid (Dab); N-methylvaline (MeVal); homocysteine (hCys); homoserine (hSer); hydroxyproline (Hyp) and homoproline (hPro). Additional non-encoded amino acids of which the polypeptides described herein may be comprised will be apparent to those of skill in the art (see, e.g., the various amino acids provided in Fasman, 1989, CRC Practical Handbook of Biochemistry and Molecular Biology, CRC Press, Boca Raton, Fla., at pp. 3-70 and the references cited therein, all of which are incorporated by reference). These amino acids may be in either the L- or D-configuration.

Those of skill in the art will recognize that amino acids or residues bearing side chain protecting groups may also comprise the polypeptides described herein. Non-limiting examples of such protected amino acids, which in this case belong to the aromatic category, include (protecting groups listed in parentheses), but are not limited to: Arg(tos), Cys(methylbenzyl), Cys (nitropyridinesulfenyl), Glu(δ-benzylester), Gln(xanthyl), Asn(N-δ-xanthyl), H is(bom), His(benzyl), His(tos), Lys(fmoc), Lys(tos), Ser(O-benzyl), Thr (O-benzyl) and Tyr(O-benzyl).

Non-encoding amino acids that are conformationally constrained of which the polypeptides described herein may be composed include, but are not limited to, N-methyl amino acids (L-configuration); 1-aminocyclopent-(2 or 3)-ene-4-carboxylic acid; pipecolic acid; azetidine-3-carboxylic acid; homoproline (hPro); and 1-aminocyclopentane-3-carboxylic acid.

As described above the various modifications introduced into the naturally occurring polypeptide to generate an engineered transaminase enzyme can be targeted to a specific property of the enzyme.

In some embodiments, the polypeptide described herein can be provided in the form of kits. The enzymes in the kits may be present individually or as a plurality of enzymes. The kits can further include reagents for carrying out the enzymatic reactions, substrates for assessing the activity of enzymes, as well as reagents for detecting the products. The kits can also include reagent dispensers and instructions for use of the kits.

In some embodiments, the polypeptides can be provided on a physical substrate. In some embodiments, the polypeptides can be provided in the form of an array in which the polypeptides are arranged in positionally distinct locations. The array can be used to test a variety of substrate compounds for conversion by the polypeptides. “Substrate,” “support,” “solid support,” “solid carrier,” or “resin” in the context of arrays refer to any solid phase material. Substrate also encompasses terms such as “solid phase,” “surface,” and/or “membrane.” A solid support can be composed of organic polymers such as polystyrene, polyethylene, polypropylene, polyfluoroethylene, polyethyleneoxy, and polyacrylamide, as well as co-polymers and grafts thereof. A solid support can also be inorganic, such as glass, silica, controlled pore glass (CPG), reverse phase silica or metal, such as gold or platinum. The configuration of a substrate can be in the form of beads, spheres, particles, granules, a gel, a membrane or a surface. Surfaces can be planar, substantially planar, or non-planar. Solid supports can be porous or non-porous, and can have swelling or non-swelling characteristics. A solid support can be configured in the form of a well, depression, or other container, vessel, feature, or location. A plurality of supports can be configured on an array at various locations, addressable for robotic delivery of reagents, or by detection methods and/or instruments.

In certain embodiments, the kits of the present disclosure include arrays comprising a plurality of different transaminase polypeptides at different addressable position, wherein the different polypeptides are different variants of a reference sequence each having at least one different improved enzyme property. Such arrays comprising a plurality of engineered polypeptides and methods of their use are described in, e.g., WO2009/008908A2.

In some embodiments, the transaminase polypeptides can be bound on a physical substrate. The transaminase polypeptide can be bound non-covalently or covalently. Various methods for conjugation to substrates, e.g., membranes, beads, glass, etc. are described in, among others, Hermanson, G. T., Bioconjugate Techniques, Second Edition, Academic Press; (2008), and Bioconjugation Protocols Strategies and Methods, In Methods in Molecular Biology, C. M. Niemeyer ed., Humana Press (2004); the disclosures of which are incorporated herein by reference.

5.4 Polynucleotides Encoding Engineered Transaminases

In another aspect, the present disclosure provides polynucleotides encoding the engineered transaminase enzymes described herein. The polynucleotides may be operatively linked to one or more heterologous regulatory sequences that control gene expression to create a recombinant polynucleotide capable of expressing the polypeptide. Expression constructs containing a heterologous polynucleotide encoding the engineered transaminase can be introduced into appropriate host cells to express the corresponding transaminase polypeptide.

Because of the knowledge of the codons corresponding to the various amino acids, availability of a protein sequence provides a description of all the polynucleotides capable of encoding the subject. The degeneracy of the genetic code, where the same amino acids are encoded by alternative or synonymous codons allows an extremely large number of nucleic acids to be made, all of which encode the improved transaminase enzymes disclosed herein. Thus, having identified a particular amino acid sequence, those skilled in the art could make any number of different nucleic acids by simply modifying the sequence of one or more codons in a way which does not change the amino acid sequence of the protein. In this regard, the present disclosure specifically contemplates each and every possible variation of polynucleotides that could be made by selecting combinations based on the possible codon choices, and all such variations are to be considered specifically disclosed for any polypeptide disclosed herein, including the amino acid sequences presented in Table 2.

In various embodiments, the codons are preferably selected to fit the host cell in which the protein is being produced. For example, preferred codons used in bacteria are used to express the gene in bacteria; preferred codons used in yeast are used for expression in yeast; and preferred codons used in mammals are used for expression in mammalian cells.

In certain embodiments, all codons need not be replaced to optimize the codon usage of the transaminases since the natural sequence will comprise preferred codons and because use of preferred codons may not be required for all amino acid residues. Consequently, codon optimized polynucleotides encoding the transaminase enzymes may contain preferred codons at about 40%, 50%, 60%, 70%, 80%, or greater than 90% of codon positions of the full length coding region.

In some embodiments, the polynucleotide encodes a transaminase polypeptide comprising an amino acid sequence that is at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more identical to the reference sequence of SEQ ID NO:2, where the polypeptide has transaminase activity and one or more of the improved properties described herein in the conversion of 3-hydroxyacetophenone to (S)-3-(1-aminoethyl)-phenol. In some embodiments, the polynucleotide encodes an engineered transaminase polypeptide comprises an amino acid sequence that has the percent identity described above and has one or more amino acid residue differences as compared to SEQ ID NO:2 at residue positions corresponding to X18, X163, X235, X244, X323, X383, X424, and X427.

In some embodiments, the polynucleotide encodes a transaminase polypeptide comprising an amino acid sequence that is at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more identical to the reference sequence of SEQ ID NO:4, where the polypeptide has transaminase activity and one or more of the improved properties described herein in the conversion of 3-hydroxyacetophenone to (S)-3-(1-aminoethyl)-phenol. In some embodiments, the polynucleotide encodes an engineered transaminase polypeptide comprises an amino acid sequence that has the percent identity described above and has one or more amino acid residue differences as compared to SEQ ID NO:4 at residue positions corresponding to X18, X163, X235, X244, X323, X383, X424, and X427.

In some embodiments, the polynucleotide comprises a nucleotide sequence encoding a transaminase polypeptide with an amino acid sequence that has at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% or more sequence identity to any of the reference engineered transaminase polypeptides described herein. Accordingly, in some embodiments, the polynucleotide encodes an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more identical to SEQ ID NO: 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, or 44, where the polypeptide has transaminase activity and one or more of the improved properties described herein in the conversion of 3-hydroxyacetophenone to (S)-3-(1-aminoethyl)-phenol. In some embodiments, the polynucleotide encodes an engineered transaminase polypeptide comprises an amino acid sequence that has the percent identity described above and has one or more amino acid residue differences as compared to SEQ ID NO:2 at residue positions corresponding to X18, X163, X235, X244, X323, X383, X424, and X427.

In some embodiments, the polynucleotides encoding the engineered transaminases are selected from SEQ ED NO: 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, and 43.

In some embodiments, the polynucleotides are capable of hybridizing under highly stringent conditions to a polynucleotide selected from SEQ ID NO: 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, or 43, or a complement thereof, and encodes a polypeptide having transaminase activity with one or more of the improved properties described herein. In some embodiments, the polynucleotide capable of hybridizing under highly stringent conditions encodes a transaminase polypeptide comprising an amino acid sequence that has one or more amino acid residue differences as compared to SEQ ID NO:2 at residue positions corresponding to X18, X163, X235, X244, X323, X383, X424, and X427, as described herein.

In some embodiments, the polynucleotides encode the polypeptides described herein but have about 80% or more sequence identity, about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% or more sequence identity at the nucleotide level to a reference polynucleotide encoding the engineered transaminase. In some embodiments, the reference polynucleotide sequence is selected from SEQ ID NO: 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, or 43.

An isolated polynucleotide encoding an improved transaminase polypeptide may be manipulated in a variety of ways to provide for expression of the polypeptide. Manipulation of the isolated polynucleotide prior to its insertion into a vector may be desirable or necessary depending on the expression vector. The techniques for modifying polynucleotides and nucleic acid sequences utilizing recombinant DNA methods are well known in the art. Guidance is provided in Sambrook et al., 2001, Molecular Cloning: A Laboratory Manual, 3^(rd) Ed., Cold Spring Harbor Laboratory Press; and Current Protocols in Molecular Biology, Ausubel. F. ed., Greene Pub. Associates, 1998, updates to 2006.

For bacterial host cells, suitable promoters for directing transcription of the nucleic acid constructs of the present disclosure, include the promoters obtained from the E. coli lac operon, Streptomyces coelicolor agarase gene (dagA), Bacillus subtilis levansucrase gene (sacB), Bacillus licheniformis alpha-amylase gene (amyL), Bacillus stearothermophilus maltogenic amylase gene (amyM), Bacillus amyloliquefaciens alpha-amylase gene (amyQ), Bacillus licheniformis penicillinase gene (penP), Bacillus subtilis xylA and xylB genes, and prokaryotic beta-lactamase gene (VIIIa-Kamaroff et al., 1978, Proc. Natl. Acad. Sci. USA 75: 3727-3731), as well as the tac promoter (DeBoer et al., 1983, Proc. Natl. Acad. Sci. USA 80: 21-25).

For filamentous fungal host cells, suitable promoters for directing the transcription of the nucleic acid constructs of the present disclosure include promoters obtained from the genes for Aspergillus oryzae TAKA amylase, Rhizomucor miehei aspartic proteinase, Aspergillus niger neutral alpha-amylase, Aspergillus niger acid stable alpha-amylase, Aspergillus niger or Aspergillus awamori glucoamylase (glaA), Rhizomucor miehei lipase, Aspergillus oryzae alkaline protease, Aspergillus oryzae triose phosphate isomerase, Aspergillus nidulans acetamidase, and Fusarium oxysporum trypsin-like protease (WO 96/00787), as well as the NA2-tpi promoter (a hybrid of the promoters from the genes for Aspergillus niger neutral alpha-amylase and Aspergillus oryzae triose phosphate isomerase), and mutant, truncated, and hybrid promoters thereof.

In a yeast host, useful promoters can be from the genes for Saccharomyces cerevisiae enolase (ENO-1), Saccharomyces cerevisiae galactokinase (GAL1), Saccharomyces cerevisiae alcohol dehydrogenase/glyceraldehyde-3-phosphate dehydrogenase (ADH2/GAP), and Saccharomyces cerevisiae 3-phosphoglycerate kinase. Other useful promoters for yeast host cells are described by Romanos et al., 1992, Yeast 8:423-488.

The control sequence may also be a suitable transcription terminator sequence, a sequence recognized by a host cell to terminate transcription. The terminator sequence is operably linked to the 3′ terminus of the nucleic acid sequence encoding the polypeptide. Any terminator which is functional in the host cell of choice may be used in the present invention.

For example, exemplary transcription terminators for filamentous fungal host cells can be obtained from the genes for Aspergillus oryzae TAKA amylase, Aspergillus niger glucoamylase, Aspergillus nidulans anthranilate synthase, Aspergillus niger alpha-glucosidase, and Fusarium oxysporum trypsin-like protease.

Exemplary terminators for yeast host cells can be obtained from the genes for Saccharomyces cerevisiae enolase, Saccharomyces cerevisiae cytochrome C(CYC1), and Saccharomyces cerevisiae glyceraldehyde-3-phosphate dehydrogenase. Other useful terminators for yeast host cells are described by Romanos et al., 1992, supra.

The control sequence may also be a suitable leader sequence, a nontranslated region of an mRNA that is important for translation by the host cell. The leader sequence is operably linked to the 5′ terminus of the nucleic acid sequence encoding the polypeptide. Any leader sequence that is functional in the host cell of choice may be used. Exemplary leaders for filamentous fungal host cells are obtained from the genes for Aspergillus oryzae TAKA amylase and Aspergillus nidulans triose phosphate isomerase. Suitable leaders for yeast host cells are obtained from the genes for Saccharomyces cerevisiae enolase (ENO-1), Saccharomyces cerevisiae 3-phosphoglycerate kinase, Saccharomyces cerevisiae alpha-factor, and Saccharomyces cerevisiae alcohol dehydrogenase/glyceraldehyde-3-phosphate dehydrogenase (ADH2/GAP).

The control sequence may also be a polyadenylation sequence, a sequence operably linked to the 3′ terminus of the nucleic acid sequence and which, when transcribed, is recognized by the host cell as a signal to add polyadenosine residues to transcribed mRNA. Any polyadenylation sequence which is functional in the host cell of choice may be used in the present invention. Exemplary polyadenylation sequences for filamentous fungal host cells can be from the genes for Aspergillus oryzae TAKA amylase, Aspergillus niger glucoamylase, Aspergillus nidulans anthranilate synthase, Fusarium oxysporum trypsin-like protease, and Aspergillus niger alpha-glucosidase. Useful polyadenylation sequences for yeast host cells are described by Guo and Sherman, 1995, Mol Cell Bio 15:5983-5990.

The control sequence may also be a signal peptide coding region that codes for an amino acid sequence linked to the amino terminus of a polypeptide and directs the encoded polypeptide into the cell's secretory pathway. The 5′ end of the coding sequence of the nucleic acid sequence may inherently contain a signal peptide coding region naturally linked in translation reading frame with the segment of the coding region that encodes the secreted polypeptide. Alternatively, the 5′ end of the coding sequence may contain a signal peptide coding region that is foreign to the coding sequence. The foreign signal peptide coding region may be required where the coding sequence does not naturally contain a signal peptide coding region.

Alternatively, the foreign signal peptide coding region may simply replace the natural signal peptide coding region in order to enhance secretion of the polypeptide. However, any signal peptide coding region which directs the expressed polypeptide into the secretory pathway of a host cell of choice may be used in the present invention.

Effective signal peptide coding regions for bacterial host cells are the signal peptide coding regions obtained from the genes for Bacillus NCIB 11837 maltogenic amylase, Bacillus stearothermophilus alpha-amylase, Bacillus licheniformis subtilisin, Bacillus licheniformis beta-lactamase, Bacillus stearothermophilus neutral proteases (nprT, nprS, nprM), and Bacillus subtilis prsA. Further signal peptides are described by Simonen and Palva, 1993, Microbiol Rev 57: 109-137.

Effective signal peptide coding regions for filamentous fungal host cells can be the signal peptide coding regions obtained from the genes for Aspergillus oryzae TAKA amylase, Aspergillus niger neutral amylase, Aspergillus niger glucoamylase, Rhizomucor miehei aspartic proteinase, Humicola insolens cellulase, and Humicola lanuginosa lipase.

Useful signal peptides for yeast host cells can be from the genes for Saccharomyces cerevisiae alpha-factor and Saccharomyces cerevisiae invertase. Other useful signal peptide coding regions are described by Romanos et al., 1992, supra.

The control sequence may also be a propeptide coding region that codes for an amino acid sequence positioned at the amino terminus of a polypeptide. The resultant polypeptide is known as a proenzyme or propolypeptide (or a zymogen in some cases). A propolypeptide can be converted to a mature active polypeptide by catalytic or autocatalytic cleavage of the propeptide from the propolypeptide. The propeptide coding region may be obtained from the genes for Bacillus subtilis alkaline protease (aprE), Bacillus subtilis neutral protease (nprT), Saccharomyces cerevisiae alpha-factor, Rhizomucor miehei aspartic proteinase, and Myceliophthora thermophila lactase (WO 95/33836).

Where both signal peptide and propeptide regions are present at the amino terminus of a polypeptide, the propeptide region is positioned next to the amino terminus of a polypeptide and the signal peptide region is positioned next to the amino terminus of the propeptide region.

It may also be desirable to add regulatory sequences, which allow the regulation of the expression of the polypeptide relative to the growth of the host cell. Examples of regulatory systems are those which cause the expression of the gene to be turned on or off in response to a chemical or physical stimulus, including the presence of a regulatory compound. In prokaryotic host cells, suitable regulatory sequences include the lac, tac, and trp operator systems. In yeast host cells, suitable regulatory systems include, as examples, the ADH2 system or GALL system. In filamentous fungi, suitable regulatory sequences include the TAKA alpha-amylase promoter, Aspergillus niger glucoamylase promoter, and Aspergillus oryzae glucoamylase promoter.

Other examples of regulatory sequences are those which allow for gene amplification. In eukaryotic systems, these include the dihydrofolate reductase gene, which is amplified in the presence of methotrexate, and the metallothionein genes, which are amplified with heavy metals. In these cases, the nucleic acid sequence encoding the polypeptide of the present invention would be operably linked with the regulatory sequence.

Thus, in another aspect, the present disclosure is also directed to a recombinant expression vector comprising a polynucleotide encoding an engineered transaminase polypeptide or a variant thereof, and one or more expression regulating regions such as a promoter and a terminator, a replication origin, etc., depending on the type of hosts into which they are to be introduced. The various nucleic acid and control sequences described above may be joined together to produce a recombinant expression vector which may include one or more convenient restriction sites to allow for insertion or substitution of the nucleic acid sequence encoding the polypeptide at such sites. Alternatively, the nucleic acid sequence of the present disclosure may be expressed by inserting the nucleic acid sequence or a nucleic acid construct comprising the sequence into an appropriate vector for expression. In creating the expression vector, the coding sequence is located in the vector so that the coding sequence is operably linked with the appropriate control sequences for expression.

The recombinant expression vector may be any vector (e.g., a plasmid or virus), which can be conveniently subjected to recombinant DNA procedures and can bring about the expression of the polynucleotide sequence. The choice of the vector will typically depend on the compatibility of the vector with the host cell into which the vector is to be introduced. The vectors may be linear or closed circular plasmids.

The expression vector may be an autonomously replicating vector, i.e., a vector that exists as an extrachromosomal entity, the replication of which is independent of chromosomal replication, e.g., a plasmid, an extrachromosomal element, a minichromosome, or an artificial chromosome. The vector may contain any means for assuring self-replication. Alternatively, the vector may be one which, when introduced into the host cell, is integrated into the genome and replicated together with the chromosome(s) into which it has been integrated. Furthermore, a single vector or plasmid or two or more vectors or plasmids which together contain the total DNA to be introduced into the genome of the host cell, or a transposon may be used.

The expression vector of the present invention preferably contains one or more selectable markers, which permit easy selection of transformed cells. A selectable marker is a gene the product of which provides for biocide or viral resistance, resistance to heavy metals, prototrophy to auxotrophs, and the like. Examples of bacterial selectable markers are the dal genes from Bacillus subtilis or Bacillus licheniformis, or markers, which confer antibiotic resistance such as ampicillin, kanamycin, chloramphenicol (Example 1) or tetracycline resistance. Suitable markers for yeast host cells are ADE2, HIS3, LEU2, LYS2, MET3, TRP1, and URA3.

Selectable markers for use in a filamentous fungal host cell include, but are not limited to, amdS (acetamidase), argB (ornithine carbamoyltransferase), bar (phosphinothricin acetyltransferase), hph (hygromycin phosphotransferase), niaD (nitrate reductase), pyrG (orotidine-5′-phosphate decarboxylase), sC (sulfate adenyltransferase), and trpC (anthranilate synthase), as well as equivalents thereof. Embodiments for use in an Aspergillus cell include the amdS and pyrG genes of Aspergillus nidulans or Aspergillus oryzae and the bar gene of Streptomyces hygroscopicus.

The expression vectors of the present invention can contain an element(s) that permits integration of the vector into the host cell's genome or autonomous replication of the vector in the cell independent of the genome. For integration into the host cell genome, the vector may rely on the nucleic acid sequence encoding the polypeptide or any other element of the vector for integration of the vector into the genome by homologous or nonhomologous recombination.

Alternatively, the expression vector may contain additional nucleic acid sequences for directing integration by homologous recombination into the genome of the host cell. The additional nucleic acid sequences enable the vector to be integrated into the host cell genome at a precise location(s) in the chromosome(s). To increase the likelihood of integration at a precise location, the integrational elements should preferably contain a sufficient number of nucleic acids, such as 100 to 10,000 base pairs, preferably 400 to 10,000 base pairs, and most preferably 800 to 10,000 base pairs, which are highly homologous with the corresponding target sequence to enhance the probability of homologous recombination. The integrational elements may be any sequence that is homologous with the target sequence in the genome of the host cell. Furthermore, the integrational elements may be non-encoding or encoding nucleic acid sequences. On the other hand, the vector may be integrated into the genome of the host cell by non-homologous recombination.

For autonomous replication, the vector may further comprise an origin of replication enabling the vector to replicate autonomously in the host cell in question. Examples of bacterial origins of replication are P15A ori (as shown in the plasmid of FIG. 5) or the origins of replication of plasmids pBR322, pUC19, pACYC177 (which plasmid has the P15A ori), or pACYC184 permitting replication in E. coli, and pUB110, pE194, pTA1060, or pAM□1 permitting replication in Bacillus. Examples of origins of replication for use in a yeast host cell are the 2 micron origin of replication, ARS1, ARS4, the combination of ARS1 and CEN3, and the combination of ARS4 and CEN6. The origin of replication may be one having a mutation which makes its functioning temperature-sensitive in the host cell (see, e.g., Ehrlich, 1978, Proc Natl Acad. Sci. USA 75:1433).

More than one copy of a nucleic acid sequence of the present invention may be inserted into the host cell to increase production of the gene product. An increase in the copy number of the nucleic acid sequence can be obtained by integrating at least one additional copy of the sequence into the host cell genome or by including an amplifiable selectable marker gene with the nucleic acid sequence where cells containing amplified copies of the selectable marker gene, and thereby additional copies of the nucleic acid sequence, can be selected for by cultivating the cells in the presence of the appropriate selectable agent.

Many of the expression vectors for use in the present invention are commercially available. Suitable commercial expression vectors include p3xFLAG™ expression vectors from Sigma-Aldrich Chemicals, St. Louis Mo., which includes a CMV promoter and hGH polyadenylation site for expression in mammalian host cells and a pBR322 origin of replication and ampicillin resistance markers for amplification in E. coli. Other suitable expression vectors are pBluescriptII SK(−) and pBK-CMV, which are commercially available from Stratagene, LaJolla Calif., and plasmids which are derived from pBR322 (Gibco BRL), pUC (Gibco BRL), pREP4, pCEP4 (Invitrogen) or pPoly (Lathe et al., 1987, Gene 57:193-201).

5.5 Host Cells for Expression of Transaminase Polypeptides

In another aspect, the present disclosure provides a host cell comprising a polynucleotide encoding an improved transaminase polypeptide of the present disclosure, the polynucleotide being operatively linked to one or more control sequences for expression of the transaminase enzyme in the host cell. Host cells for use in expressing the polypeptides encoded by the expression vectors of the present invention are well known in the art and include but are not limited to, bacterial cells, such as E. coli, Vibrio fluvialis, Streptomyces and Salmonella typhimurium cells; fungal cells, such as yeast cells (e.g., Saccharomyces cerevisiae or Pichia pastoris (ATCC Accession No. 201178)); insect cells such as Drosophila S2 and Spodoptera Sf9 cells; animal cells such as CHO, COS, BHK, 293, and Bowes melanoma cells; and plant cells. Appropriate culture mediums and growth conditions for the above-described host cells are well known in the art.

Polynucleotides for expression of the transaminase may be introduced into cells by various methods known in the art. Techniques include among others, electroporation, biolistic particle bombardment, liposome mediated transfection, calcium chloride transfection, and protoplast fusion. Various methods for introducing polynucleotides into cells will be apparent to the skilled artisan.

An exemplary host cell is Escherichia coli W3110 (ΔfhuA). The expression vector was created by operatively linking a polynucleotide encoding an improved transaminase into the plasmid pCK110900I operatively linked to the lac promoter under control of the lad repressor. The expression vector also contained the P15a origin of replication and the chloramphenicol resistance gene.

5.6 Methods of Generating Engineered Transaminase Polypeptides.

In some embodiments, to make the improved polynucleotides and polypeptides of the present disclosure, the naturally-occurring transaminase enzyme that catalyzes the transamination reaction is obtained (or derived) from Vibrio fluvialis. In some embodiments, the parent polynucleotide sequence is codon optimized to enhance expression of the transaminase in a specified host cell. The parental polynucleotide sequence encoding the wild-type polypeptide of Vibrio fluvialis is described in Shin et al., 2003, “Purification, characterization, and molecular cloning of a novel amine:pyruvate transaminase from Vibrio fluvialis JS17,” Appl. Microbiol. Biotechnol. 61(5-6):463-471.

The engineered transaminases can be obtained by subjecting the polynucleotide encoding the naturally occurring transaminase to mutagenesis and/or directed evolution methods, as discussed above. An exemplary directed evolution technique is mutagenesis and/or DNA shuffling as described in Stemmer, 1994, Proc Natl Acad Sci USA 91:10747-10751; WO 95/22625; WO 97/0078; WO 97/35966; WO 98/27230; WO 00/42651; WO 01/75767 and U.S. Pat. No. 6,537,746. Other directed evolution procedures that can be used include, among others, staggered extension process (StEP), in vitro recombination (Zhao et al., 1998, Nat. Biotechnol. 16:258-261), mutagenic PCR (Caldwell et al., 1994, PCR Methods Appl. 3:S136-S140), and cassette mutagenesis (Black et al., 1996, Proc Natl Acad Sci USA 93:3525-3529). Mutagenesis and directed evolution techniques useful for the purposes herein are also described in the following references: Ling, et al., 1997, Anal. Biochem. 254(2):157-78; Dale et al., 1996, “Oligonucleotide-directed random mutagenesis using the phosphorothioate method,” In Methods Mol. Biol. 57:369-74; Smith, 1985, Ann. Rev. Genet. 19:423-462; Botstein et al., 1985, Science 229:1193-1201; Carter, 1986, Biochem. J. 237:1-7; Kramer et al., 1984, Cell, 38:879-887; Wells et al., 1985, Gene 34:315-323; Minshull et al., 1999, Curr Opin Chem Biol 3:284-290; Christians et al., 1999, Nature Biotech 17:259-264; Crameri et al., 1998, Nature 391:288-291; Crameri et al., 1997, Nature Biotech 15:436-438; Zhang et al., 1997, Proc Natl Acad Sci USA 94:45-4-4509; Crameri et al., 1996, Nature Biotech 14:315-319; Stemmer, 1994, Nature 370:389-391; Stemmer, 1994, Proc Natl Acad Sci USA 91:10747-10751; WO 95/22625; WO 97/0078; WO 97/35966; WO 98/27230; WO 00/42651; WO 01/75767 and U.S. Pat. No. 6,537,746. All publications are incorporated herein by reference.

The clones obtained following mutagenesis treatment can be screened for engineered transaminases having a desired improved enzyme property. Measuring enzyme activity from the expression libraries can be performed using the standard biochemistry techniques, such as HPLC analysis following OPA derivitization of the product amine.

Where the improved enzyme property desired is thermostability, enzyme activity may be measured after subjecting the enzyme preparations to a defined temperature and measuring the amount of enzyme activity remaining after heat treatments. Clones containing a polynucleotide encoding a transaminase are then isolated, sequenced to identify the nucleotide sequence changes (if any), and used to express the enzyme in a host cell.

Where the sequence of the engineered polypeptide is known, the polynucleotides encoding the enzyme can be prepared by standard solid-phase methods, according to known synthetic methods. In some embodiments, fragments of up to about 100 bases can be individually synthesized, then joined (e.g., by enzymatic or chemical litigation methods, or polymerase mediated methods) to form any desired continuous sequence. For example, polynucleotides and oligonucleotides of the invention can be prepared by chemical synthesis using, e.g., the classical phosphoramidite method described by Beaucage et al., 1981, Tet Lett 22:1859-69, or the method described by Matthes et al., 1984, EMBO J. 3:801-05, e.g., as it is typically practiced in automated synthetic methods. According to the phosphoramidite method, oligonucleotides are synthesized, e.g., in an automatic DNA synthesizer, purified, annealed, ligated and cloned in appropriate vectors. In addition, essentially any nucleic acid can be obtained from any of a variety of commercial sources.

Engineered transaminase enzymes expressed in a host cell can be recovered from the cells and or the culture medium using any one or more of the well known techniques for protein purification, including, among others, lysozyme treatment, sonication, filtration, salting-out, ultra-centrifugation, and chromatography. Suitable solutions for lysing and the high efficiency extraction of proteins from bacteria, such as E. coli, are commercially available under the trade name CelLytic B™ from Sigma-Aldrich of St. Louis Mo.

Chromatographic techniques for isolation of the transaminase polypeptide include, among others, reverse phase chromatography high performance liquid chromatography, ion exchange chromatography, gel electrophoresis, and affinity chromatography. Conditions for purifying a particular enzyme will depend, in part, on factors such as net charge, hydrophobicity, hydrophilicity, molecular weight, molecular shape, etc., and will be apparent to those having skill in the art.

In some embodiments, affinity techniques may be used to isolate the improved transaminase enzymes. For affinity chromatography purification, any antibody which specifically binds the transaminase polypeptide may be used. For the production of antibodies, various host animals, including but not limited to rabbits, mice, rats, etc., may be immunized by injection with a transaminase polypeptide, or a fragment thereof. The transaminase polypeptide or fragment may be attached to a suitable carrier, such as BSA, by means of a side chain functional group or linkers attached to a side chain functional group. Various adjuvants may be used to increase the immunological response, depending on the host species, including but not limited to Freund's (complete and incomplete), mineral gels such as aluminum hydroxide, surface active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanin, dinitrophenol, and potentially useful human adjuvants such as BCG (bacilli Calmette Guerin) and Corynebacterium parvum.

5.7 Methods of Using the Engineered Transaminase Enzymes and Compounds Prepared Therewith

In another aspect, the transaminases described herein can be used in a process for carrying out transaminase reactions in which an amino group from an amino donor of general Formula IV is transferred to an amino acceptor (ketone substrate) of general Formula III to produce a chiral amine. Generally, the method for performing the transamination reaction can comprise contacting or incubating an amino donor of Formula IV and an amino acceptor of Formula III with an engineered transaminase polypeptide of the disclosure under reaction conditions suitable for converting the amine acceptor to the chiral amine in stereomeric excess (as shown in Scheme 2):

In some embodiments, each of R¹, R², R³ and R⁴, when taken independently, can be an alkyl, an alkylaryl group, or aryl group which is unsubstituted or substituted with one or more enzymatically non-inhibiting groups, where R¹ is different from R² in structure or chirality, or R¹ and R², taken together, are a hydrocarbon chain of 4 or more carbon atoms containing a center of chirality. In some embodiments, the alkyl group can be a substituted or unsubstituted branched or straight chain alkyl. R³ may be the same or different from R⁴ in structure or chirality. In some embodiments, R³ and R⁴, taken together, may form a ring that is unsubstituted, substituted, or fused to other rings. In some embodiments, the rings can be substituted or unsubstituted cycloalkyl or heterocycloalkyl. In some embodiments for R³ and R⁴, the alkyl, either alone or as a substituted or unsubstituted alkylaryl is a lower alkyl.

In some embodiments, the transaminase polypeptides can be used in a process for the conversion of the substrate compound (1), 3-hydroxyacetophenone, to the product of compound (2), (S)-3-(1-aminoethyl)-phenol (see Scheme 1), where the product is formed in enantiomeric excess. The process for preparing (S)-3-(1-aminoethyl)-phenol in enantiomeric excess can comprise contacting 3-hydroxyacetophenone with a transaminase polypeptide described herein in presence of an amino donor under suitable reaction conditions. In the process, any of the engineered transaminases described herein can be used to produce the chiral amine product (e.g., (S)-3-(1-aminoethyl)-phenol). As described above, the engineered polypeptide capable of converting the substrate 3′-hydroxyacetophenone to the product (S)-3-(1-aminoethyl)-phenol in enantiomeric excess comprises an amino acid sequence that is at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more identical to the reference sequence of SEQ ID NO:2, where the amino acid sequence has one or more residue differences as compared to the amino acid sequence of SEQ ID NO:2.

In some embodiments, the engineered polypeptide capable of converting the substrate 3′-hydroxyacetophenone to the product (S)-3-(1-aminoethyl)-phenol in enantiomeric excess comprises an amino acid sequence that is at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more identical to the reference sequence of SEQ ID NO:4, where the amino acid sequence has one or more residue differences as compared to the amino acid sequence of SEQ ID NO:4.

In some embodiments, the engineered polypeptide capable of converting the substrate 3′-hydroxyacetophenone to the product (S)-3-(1-aminoethyl)-phenol in enantiomeric excess comprises an amino acid sequence that is at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more identical to the reference sequence selected from SEQ ID NO: 8, 10, 12, 14, 15, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, and 44. In particular, the engineered transaminase polypeptide can comprise an amino acid sequence that is at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more identical to the reference sequence of SEQ ID NO:8, 14, or 32.

In the embodiments disclosed herein, the engineered transaminases have one or more residue differences have one or more residue differences as compared to the amino acid sequence of SEQ ID NO:2 or a reference engineered transaminase polypeptide, such as the reference polypeptide of SEQ ID NO:4. In some embodiments, the transaminases have one or more residue differences at residue positions selected from X18, X21, X31, X113, X122, X130; X133; X146; X147, X153, X163, X164; X167; X168; X174;X233; X235, X244; X286; X293, X316, X318; X323, X332, X375, X383, X418, X424, and X427. The transaminases can have in combination with the residue differences at the foregoing residue positions, one or more residue differences at residue positions selected from X9, X45, X86, X177, X211, X294, X324, and X391.

Guidance in choosing an engineered transaminase for a specific amine acceptor substrate is provided in the descriptions herein, such as in Table 2, which shows the activities of various engineered transaminases. Exemplary transaminases capable of converting the substrate 3′-hydroxyacetophenone to the product (S)-3-(1-aminoethyl)-phenol in enantiomeric excess can be a polypeptide comprising an amino acid sequence selected from SEQ ID NO: 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26. 28, 30, 32, 34, 36, 38, 40, 42, and 44.

In some embodiments of the process, the amino donor comprises a compound of Formula IV (see Scheme 2), selected from isopropylamine (2-aminopropane or IPM), putrescine, L-lysine, α-phenethylamine, D-alanine, L-alanine, or D,L-alanine, or D,L-ornithine. In some embodiments, the amino donor is selected from the group consisting of IPM, putrescine, L-lysine, D- or L-alanine. In some embodiments, the amino donor is IPM.

Suitable reaction conditions using the engineered transaminase polypeptides also typically require a cofactor, although in many embodiments the engineered transaminases disclosed herein require far less cofactor than reactions catalyzed with wild-type transaminase enzymes. As used herein, the term “cofactor” refers to a non-protein compound that operates in combination with a transaminase enzyme. Cofactors useful in the methods using the engineered transaminase enzymes described herein include, but are not limited to, pyridoxal-5′-phosphate (also known as pyridoxal-phosphate, PLP, P5P). In some embodiments, a different member of the vitamin B₆ family, such as pyridoxine, is used in place of PLP. In some embodiments, the cofactor PLP is present naturally in the cell extract and does not need to be supplemented. In embodiments of the methods, using partially purified, or purified transaminase enzyme, the suitable reaction conditions comprise cofactor added to the enzyme reaction mixture. In some embodiments, the cofactor is added either at the beginning of the reaction and/or additional cofactor is added during the reaction.

In some embodiments of the method, the suitable reaction conditions comprise the presence of the reduced cofactor, nicotinamide adenine dinucleotide (NADH), which can act to limit the inactivation of the transaminase enzyme (see e.g., van Ophem et al., 1998, Biochemistry 37(9):2879-88). In such embodiments where NADH is present, a cofactor regeneration system, such as glucose dehydrogenase (GDH) and glucose or formate dehydrogenase and formate can be used to regenerate the NADH in the reaction medium.

The present disclosure also contemplates ranges of suitable reaction conditions that can be used in the methods, including but not limited to ranges of pH, temperature, buffer, solvent system, substrate loading, polypeptide loading, cofactor loading, atmosphere, and reaction time. The present disclosure also contemplates that the methods comprising the biocatalytic conversion compound (1) to compound (2) using an engineered transaminase polypeptide of the disclosure can further comprise chemical steps of compound (2) product work-up, extraction, isolation, purification, and/or crystallization, each of which can be carried out under a range of conditions.

Further suitable reaction conditions for carrying out the biocatalytic conversion compound (1) to compound (2) using an engineered transaminase polypeptide described herein can be readily optimized by routine experimentation that includes, but is not limited to, contacting the engineered transaminase polypeptide and substrate (1) under experimental reaction conditions of concentration, pH, temperature, solvent conditions, and detecting the production of compound (2), for example, using the methods described in the Examples provided herein.

In some embodiments of the process, the initial concentration of compound (1) substrate (i.e., substrate loading) used in the process is related, among other, to the amount of enzyme used, the solubility of the substrate in the solvent, and the % conversion desired. In some embodiments, the substrate 3-hydroxyacetophenone can be present at an initial concentration of about 5 g/L to about 250 g/L. In some embodiments, the 3-hydroxyacetophenone can be present at an initial concentration of about 10 g/L to about 205 g/L.

In some embodiments, the methods for preparing compound (2) of the present disclosure can be carried out wherein the reaction conditions comprise compound (1) substrate loading of at least about 20 g/L, about 25 g/L, about 30 g/L, about 40 g/L, about 50 g/L, about 75 g/L, about 100 g/L, about 150 g/L, about 200 g/L, about 250 g/L or even greater. In certain embodiments, methods for preparing compound (2) of the present disclosure can be carried out wherein the reaction conditions comprise compound (1) substrate loading of about 20-250 g/L, about 25-200 g/L, about 40-150 g/L, about 50-150 g/L, about 20 g/L, about 25 g/L, about 30 g/L, about 40 g/L, about 50 g/L, about 100 g/L, about 150 g/L or about 200 g/L. The values for substrate loadings provided herein are based on the molecular weight of compound (1), however it also contemplated that the equivalent molar amounts of various hydrates and salts of compound (1) also can be used in the methods.

In carrying out the transamination reactions described herein, the engineered transaminase polypeptide may be added to the reaction mixture in the form of a purified enzyme, whole cells transformed with gene(s) encoding the enzyme, and/or as cell extracts and/or lysates of such cells. Whole cells transformed with gene(s) encoding the engineered transaminase enzyme or cell extracts, lysates thereof, and isolated enzymes may be employed in a variety of different forms, including solid (e.g., lyophilized, spray-dried, and the like) or semisolid (e.g., a crude paste). The cell extracts or cell lysates may be partially purified by precipitation (ammonium sulfate, polyethyleneimine, heat treatment or the like, followed by a desalting procedure prior to lyophilization (e.g., ultrafiltration, dialysis, and the like). Any of the cell preparations may be stabilized by crosslinking using known crosslinking agents, such as, for example, glutaraldehyde or immobilization to a solid phase (e.g., Eupergit C, and the like).

The gene(s) encoding the engineered transaminase polypeptides can be transformed into host cell separately or together into the same host cell. For example, in some embodiments one set of host cells can be transformed with gene(s) encoding one engineered transaminase polypeptide and another set can be transformed with gene(s) encoding another engineered transaminase polypeptide. Both sets of transformed cells can be utilized together in the reaction mixture in the form of whole cells, or in the form of lysates or extracts derived therefrom. In other embodiments, a host cell can be transformed with gene(s) encoding multiple engineered transaminase polypeptide. In some embodiments the engineered polypeptides can be expressed in the form of secreted polypeptides and the culture medium containing the secreted polypeptides can be used for the transaminase reaction.

In some embodiments, the engineered transaminase polypeptide is present at sufficient amounts to carry out the conversion of the substrate to product to the desired percent conversion of substrate to product in a defined time period under a defined process condition. In some embodiments, conversion yields of the chiral amine product generated in the reaction mixture are generally greater than about 50%, may also be greater than about 60%, may also be greater than about 70%, may also be greater than about 80%, may also be greater than 90%, and are often greater than about 97%.

The improved enzymatic activity of the engineered transaminase polypeptides of the present disclosure in the conversion of compound (1) to compound (2) provides for methods wherein higher percentage conversion can be achieved with lower concentrations of the engineered polypeptide. The use of lower concentration of the engineered polypeptide in a method comprising a conversion of compound (1) to compound (2) also reduces the amount of residual protein that may need to be removed in subsequent steps for purification of compound (2). In some embodiments, the methods for preparing compound (2) of the present disclosure can be carried out wherein the reaction conditions comprise an engineered polypeptide concentration of about 0.1 to about 15 g/L, about 0.5 to about 10 g/L, about 1.0 to about 5 g/L, about 2 to about 5 g/L, about 20 g/L, about 10 g/L, about 5, g/L, about 3 g/L, about 2 g/L, about 1.5 g/L, about 1.0 g/L, about 0.75 g/L, or even lower concentration.

In some embodiments, the method of preparing compound (2) using an engineered transaminase polypeptide of the disclosure is carried out wherein the suitable reaction conditions comprise the amino donor at a concentration of at least about 0.5 M, at least about 1.0 M, at least about 2.5 M, at least about 5.0 M, at least about 7.5 M, at least about 10.0 M, or more. In some embodiments, the amino donor is IPM and the suitable reaction conditions comprise an IPM concentration of at least about 0.5 M, at least about 1.0 M, at least about 2.5 M, at least about 5.0 M, at least about 7.5 M, at least about 10.0 M, or more.

In certain embodiments, the temperature of the suitable reaction conditions can be chosen to maximize the reaction rate at higher temperatures while maintaining the activity of the enzyme for sufficient duration for efficient conversion of the substrate to the product. Where higher temperatures are used, polypeptides with increased thermostability can be selected to carry out the process.

The engineered polypeptides of the present disclosure have increased thermal stability relative to the naturally occurring transaminase polypeptide of SEQ ID NO: 2. This allows the engineered polypeptides to be used in methods for converting compound (1) to compound (2) at higher temperatures which can result in increased conversion rates and improved substrate solubility characteristics for the reaction, although substrate or product degradation at higher temperatures can contribute to decreased process yields. In certain embodiments, the method can be carried out wherein the reaction conditions comprise a temperature of about 15° C. to about 60° C., about 20° C. to about 55° C., about 30° C. to about 50° C., about 40° C. to about 60° C., about 40° C. to about 50° C., about 45° C. to about 55° C., about 25° C., about 30° C., about 35° C., about 40° C., about 45° C., about 50° C., about 55° C., or about 60° C., or more. In certain embodiments, the temperature during the enzymatic reaction can be maintained at a temperature, such as ambient temperature (e.g., 25° C.), about 30° C., about 35° C., about 40° C., about 45° C., about 50° C., about 55° C., or about 60° C., or more. In some embodiments, the temperature during the enzymatic reaction can be adjusted over a temperature profile during the course of the reaction.

In certain embodiments, the methods for preparing compound (2) using the engineered transaminase polypeptides of the present disclosure can be carried out with the pH of the reaction mixture may be maintained at a desired pH or within a desired pH range by the addition of an acid or a base during the course of the reaction. In certain embodiments, the pH of the reaction mixture may change or be changed during the course of the reaction. Thus, it is contemplated that in some embodiments the pH may be controlled by using an aqueous solvent that comprises a buffer. Suitable buffers to maintain desired pH ranges are known in the art and include, for example, phosphate buffer, triethanolamine buffer, and the like. Combinations of buffering and acid or base addition may also be used.

The methods for preparing compound (2) of the present disclosure are generally carried out in a solvent. Suitable solvents include water, aqueous buffer solutions, organic solvents, and/or co-solvent systems, which generally comprise aqueous solvents and organic solvents.

The aqueous solvent (water or aqueous co-solvent system) may be pH-buffered or unbuffered. Generally, suitable reaction conditions for preparing compound (2) using an engineered transaminase polypeptide of the present disclosure comprise a pH of about 11 or below, usually in the range of from about pH 5 to about pH 11. In some embodiments, the suitable reaction conditions comprise a pH of about 10 or below, usually in the range of from about pH 5 to about pH 10. In some embodiments, the suitable reaction conditions comprise a pH of about 9 or below, often in the range of from about pH 5 to about 9, and usually in the range of from about 6 to about 8. In some embodiments, the suitable reaction conditions comprise a pH of about 7.2 to about 7.8, about 7.4 to about 7.6, or about pH 7.5, or in some embodiments a neutral pH, i.e., about 7. Accordingly, in certain embodiments, the methods for preparing compound (2) of the present disclosure can be carried out wherein the reaction conditions comprise a pH of about 5.0 to about 11.0, a pH of about 6.0 to about 10.5, a pH of about 6.5 to about 10.0, a pH of about 7.0 to about 9.5, a pH of about 7.0 to about 9.0, a pH of about 7.0 to about 8.5, or a pH of about 7.2 to about 7.8, or about pH 7.5.

During the course of the transamination reactions, the pH of the reaction mixture may change. The pH of the reaction mixture may be maintained at a desired pH or within a desired pH range by the addition of an acid or a base during the course of the reaction. Alternatively, the pH may be controlled by using an aqueous solvent that comprises a buffer. Suitable buffers to maintain desired pH ranges are known in the art and include, for example, phosphate buffer, triethanolamine buffer, and the like. Combinations of buffering and acid or base addition may also be used. In some embodiments, the buffer is TEA (e.g., about 0.025 M to about 0.25 M TEA). In some embodiments, the reaction conditions comprise water as a suitable solvent with no buffer present.

In some embodiments, the methods for preparing compound (1) using an engineered transaminase polypeptide described are generally carried out in an aqueous co-solvent system comprising an organic solvent (e.g., ethanol, isopropanol (IPA), dimethyl sulfoxide (DMSO), ethyl acetate, butyl acetate, 1-octanol, heptane, octane, methyl t-butyl ether (MTBE), toluene, and the like), ionic liquids (e.g., 1-ethyl 4-methylimidazolium tetrafluoroborate, 1-butyl-3-methylimidazolium tetrafluoroborate, 1-butyl-3-methylimidazolium hexafluorophosphate, and the like). Exemplary aqueous co-solvent systems comprises water and one or more organic solvent. In general, an organic solvent component of an aqueous co-solvent system is selected such that it does not completely inactivate the transaminase enzyme. Appropriate co-solvent systems can be readily identified by measuring the enzymatic activity of the specified engineered transaminase enzyme with a defined substrate of interest in the candidate solvent system, utilizing an enzyme activity assay, such as those described herein.

The organic solvent component of an aqueous co-solvent system may be miscible with the aqueous component, providing a single liquid phase, or may be partly miscible or immiscible with the aqueous component, providing two liquid phases. Generally, when an aqueous co-solvent system is employed, it is selected to be biphasic, with water dispersed in an organic solvent, or vice-versa. Generally, when an aqueous co-solvent system is utilized, it is desirable to select an organic solvent that can be readily separated from the aqueous phase. In general, the ratio of water to organic solvent in the co-solvent system is typically in the range of from about 1% to about 99% (v/v) organic solvent to water. In certain embodiments, the co-solvent system comprises about 95% (v/v) to about 80% (v/v) of an aqueous buffer solution (e.g., about 0.1 M TEA) and about 5% to about 20% of an organic solvent solution. The co-solvent system may be pre-formed prior to addition to the reaction mixture, or it may be formed in situ in the reaction vessel.

The solid reactants (e.g., enzyme, salts, etc.) may be provided to the reaction in a variety of different forms, including powder (e.g., lyophilized, spray dried, and the like), solution, emulsion, suspension, and the like. The reactants can be readily lyophilized or spray dried using methods and equipment that are known to those having ordinary skill in the art. For example, the protein solution can be frozen at −80° C. in small aliquots, then added to a pre-chilled lyophilization chamber, followed by the application of a vacuum.

The quantities of reactants used in the transamination reaction will generally vary depending on the quantities of product desired, and concomitantly the amount of transaminase substrate employed. Those having ordinary skill in the art will readily understand how to vary these quantities to tailor them to the desired level of productivity and scale of production. In general, the transaminase substrates are kept at levels that achieve essentially complete or near complete conversion of the substrates into products.

In some embodiments, the order of addition of reactants is not critical. The reactants may be added together at the same time to a solvent (e.g., monophasic solvent, biphasic aqueous co-solvent system, and the like), or alternatively, some of the reactants may be added separately, and some together at different time points. For example, the cofactor, transaminase, and transaminase substrate may be added first to the solvent.

For improved mixing efficiency when an aqueous co-solvent system is used, the transaminase, and cofactor may be added and mixed into the aqueous phase first. The organic phase may then be added and mixed in, followed by addition of the transaminase substrate. Alternatively, the transaminase substrate may be premixed in the organic phase, prior to addition to the aqueous phase

The transamination reaction is generally allowed to proceed until essentially complete, or near complete, transformation of substrate is obtained. Transformation of substrate to product can be monitored using known methods by detecting substrate and/or product. Suitable methods include gas chromatography, HPLC, and the like. Conversion yields of the chiral amine product generated in the reaction mixture are generally greater than about 50%, may also be greater than about 60%, may also be greater than about 70%, may also be greater than about 80%, may also be greater than 90%, and are often greater than about 97%.

In some embodiments, the methods for preparing compound (2) using an engineered transaminase polypeptide under suitable reaction conditions results in at least about 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or greater conversion of compound (1) to compound (2) in about 48 h or less, in about 36 h or less, in about 24 h or less, or even less time.

In some embodiments of the methods, the suitable reaction conditions comprise a substrate loading of compound (1) of at least about 20 g/L, 30 g/L, 40 g/L, 50 g/L, 60 g/L, 70 g/L, 100 g/L, or more, and wherein the method results in at least about 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or greater conversion of compound (1) to compound (2) in about 48 h or less, in about 36 h or less, or in about 24 h or less. Additionally, in some embodiments providing high conversion rates of compound (1) to compound (2) the suitable reaction conditions comprise an amino donor which is isopropylamine or isopropylamine acetate at a concentration of at least about 0.5 M, at least about 1.0 M, at least about 2.5 M, at least about 5.0 M, at least about 7.5 M, at least about 10.0 M, or more. Due to the high efficiency of the engineered transaminase polypeptides, in some embodiments of the methods providing high conversion rates, the suitable reaction conditions further comprise an engineered polypeptide concentration of about 0.1 to about 15 g/L, about 0.5 to about 10 g/L, about 1.0 to about 5 g/L, about 2 to about 5 g/L.

The engineered transaminase polypeptides of the present disclosure when used in the methods for preparing compound (2) under suitable reaction conditions result in an enantiomeric excess of compound (2) of at least 97%, 98, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9%.

In a further embodiment of the methods for converting compound (1) to compound (2) using the engineered transaminase polypeptides, the suitable reaction conditions comprise an initial substrate loading to the reaction solution which is then contacted by the polypeptide. This reaction solution is the further supplemented with additional substrate of compound (1) as a continuous addition over time at a rate of at least about 1 g/L/h, at least about 2 g/L/h, at least about 4 g/L/h, at least about 6 g/L/h, or higher. Thus, according to these suitable reaction conditions polypeptide is added to a solution having an initial substrate loading of at least about 20 g/L, 30 g/L, or 40 g/L. This addition of polypeptide is then followed by continuous addition of further substrate to the solution at a rate of about 2 g/L/h, 4 g/L/h, or 6 g/L/h until a much higher final substrate loading of at least about 30 g/L, 40 g/L, 50 g/L, 60 g/L, 70 g/L, 100 g/L, 150 g/L, 200 g/L or more, is reached. Accordingly, in some embodiments of the method, the suitable reaction conditions comprise addition of the polypeptide to a solution having an initial substrate loading of at least about 20 g/L, 30 g/L, or 40 g/L followed by addition of further substrate to the solution at a rate of about 2 g/L/h, 4 g/L/h, or 6 g/L/h until a final substrate loading of at least about 30 g/L, 40 g/L, 50 g/L, 60 g/L, 70 g/L, 100 g/L or more, is reached. This substrate supplementation reaction condition allows for higher substrate loadings to be achieved while maintaining high rates of conversion of compound (1) to compound (2) of at least about 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or greater. In some embodiments of this method, the further substrate added is in a solution comprising isopropylamine or isopropylamine acetate at a concentration of at least about 0.5 M, at least about 1.0 M, at least about 2.5 M, at least about 5.0 M, at least about 7.5 M, at least about 10.0 M.

In some embodiments, the methods for preparing compound (2) using an engineered transaminase polypeptide comprises the following suitable reaction conditions: (1) substrate loading of about 25-200 g/L compound (1); (2) polypeptide concentration of about 1.0-15 g/L; (3) IPM concentration of about 0.1-10 M; (4) PLP cofactor at a concentration of about 0.1-0.3 g/L; (5) about pH 5.0-10.0; and (6) temperature of about 30-60° C.

In some embodiments, the methods for preparing compound (2) using an engineered transaminase polypeptide comprises the following suitable reaction conditions: (1) substrate loading of about 25-75 g/L compound (1); (2) polypeptide concentration of about 1.0-15 g/L; (3) IPM concentration of about 0.5-2.5 M; (4) PLP cofactor at a concentration of about 0.1-0.3 g/L; (5) about pH 7.0-8.0; and (6) temperature of about 35-45° C.

In some embodiments, the methods for preparing compound (2) using an engineered transaminase polypeptide comprises the following suitable reaction conditions: (1) substrate loading of about 25-75 g/L compound (1); (2) polypeptide concentration of about 1.0-15 g/L; (3) IPM concentration of about 0.5-2.5 M; (4) PLP cofactor at a concentration of about 0.1-0.3 g/L; (5) about pH 7.0-8.0; and (6) temperature of about 35-45° C.

In some embodiments of the method for enantiomeric enrichment of a chiral amine, additional quantities of the amino acceptor can be added (up to saturation) and/or the amino acceptor (ketone) formed can be continuously removed from the reaction mixture. Conversely, when the undesired chiral form of the amine is converted to the amino acceptor (ketone) byproduct and the desired chiral form is not, the latter can be readily isolated by conventional techniques. A partial separation can be effected by acidification, extraction with a hydrocarbon such as −MTBE to remove the ketone, rendering the aqueous phase basic, and re-extraction with a hydrocarbon such as MTBE. When, on the other hand, both chiral forms of the amine are desired, the form which is converted to the ketone can be removed from the reaction mixture (or from the aqueous phase in a two phase mixture) and independently subjected to the action of an omega-transaminase in the presence of an amino donor to generate the same chiral form which was initially converted to the ketone.

In some embodiments of the processes above, the step in the process can further comprise removal of the carbonyl by-product formed from the amino group donor when the amino group is transferred to the amino group acceptor. Such removal in situ can reduce the rate of the reverse reaction such that the forward reaction dominates and more substrate is then converted to product.

Removal of the carbonyl by-product can be carried in a number of ways. Where the amino group donor is an amino acid, such as alanine, the carbonyl by product, a keto acid, can be removed by reaction with a peroxide (see, e.g., US 2008/0213845, incorporated herein by reference). Peroxides which can be used include, among others, hydrogen peroxide; peroxyacids (peracids) such as peracetic acid (CH₃CO₃H), trifluoroperacetic acid and metachloroperoxybenzoic acid; organic peroxides such as t-butyl peroxide ((CH₃)₃COOH), or other selective oxidants such as tetrapropylammonium perruthenate, MnO₂, KMnO₄, ruthenium tetroxide and related compounds. Alternatively, pyruvate removal can be achieved via its reduction to lactate by employing lactate dehydrogenase to shift equilibrium to the product amine (see, e.g., Koszelewski et al., 2008, Adv. Syn. Catal. 350: 2761-2766). Pyruvate removal can also be achieved via its decarboxylation to carbon dioxide acetaldehyde by employing pyruvate decarboxylase (see, e.g., Höhne et al., 2008, Chem Bio Chem 9: 363-365).

In some embodiments, where the choice of the amino donor results in a carbonyl by-product that has a vapor pressure higher than water (e.g., a low boiling co-product such as a volatile organic carbonyl compound), the carbonyl by-product can be removed by sparging the reaction solution with a non-reactive gas or by applying a vacuum to lower the reaction pressure and removing the carbonyl by-product present in the gas phase. A non-reactive gas is any gas that does not react with the reaction components. Various non-reactive gases include nitrogen and noble gases (e.g., inert gases). In some embodiments, the non-reactive gas is nitrogen gas.

In some embodiments, the amino donor used in the process is isopropylamine (IPM), which forms the carbonyl by-product acetone upon transfer of the amino group to the amino group acceptor. The acetone can be removed by sparging with nitrogen gas or applying a vacuum to the reaction solution and removing the acetone from the gas phase by an acetone trap, such as a condenser or other cold trap. Alternatively, the acetone can be removed by reduction to isopropanol using a ketoreductase.

In some embodiments of the processes above where the carbonyl by-product is removed, the corresponding amino group donor can be added during the transamination reaction to replenish the amino group donor and/or maintain the pH of the reaction. Replenishing the amino group donor also shifts the equilibrium towards product formation, thereby increasing the conversion of substrate to product. Thus, in some embodiments wherein the amino group donor is isopropylamine and the acetone product is removed in situ, isopropylamine can be added to the solution to replenish the amino group donor lost during the acetone removal and to maintain the pH of the reaction (e.g., at about 8.5).

Alternatively, in embodiments where an amino acid is used as amino group donor, the keto acid carbonyl by-product can be recycled back to the amino acid by reaction with ammonia and NADH using an appropriate amino acid dehydrogenase enzyme, thereby replenishing the amino group donor.

In some embodiments any of the above described methods for the conversion of compound (1) to compound (2) can be carried out wherein the method comprises contacting an analog of compound (1) with an engineered transaminase polypeptide of the present disclosure (e.g., as described in Table 2 and elsewhere herein) in the presence of an amino donor under suitable reaction conditions, thereby resulting in the preparation of the chiral amine of the corresponding analog of product compound (2) in enantiomeric excess. Suitable reactions conditions for the conversion of analogs of compound (1) to the chiral amine of the corresponding analogs of compound (2) can be the same as used for compound (1) or determined by the ordinary artisan based on the known properties of the analog compounds and routine experimentation.

Accordingly, in some embodiments the methods for the conversion of an analog of compound (1) to an analog of compound (2) can be carried out wherein the analog of compound (1) is a compound of Formula I

wherein R is a hydroxyl protecting group, and whereby the analog of compound (2) prepared is a compound of Formula II

wherein R is the same hydroxyl protecting group.

In some embodiments of the methods, the hydroxyl protecting group of R is selected from selected from the group consisting of acetyl, benzyl, benzoyl, methyl, methoxy, tert-butyloxycarbonyl, para-methoxybenzyl, benzylidine, dimethylacetal, silyl, tert-butyl-diphenylsilyl, and trimethylsilyl. In some embodiments, the silyl hydroxyl protecting group is —Si—(R^(a))(R^(b))(R^(c)) and R^(a), R^(b), and R^(c) are each independently selected from the group consisting of C₁-C₆ alkyl, phenyl, acetyl, and benzyl groups. Other examples of hydroxyl protecting groups that may be the R group of compounds of Formula II undergoing the biocatalytic methods of the present disclosure can be found in P. G. M. Wuts and T. W. Greene, “Greene's Protective Groups in Organic Synthesis—Fourth Edition,” John Wiley and Sons, New York, N.Y., 2007, Chapter 7 (“Greene”).

In further embodiments, any of the above described methods for the conversion of compound (1) (or an analog of compound (1)) to compound (2) (or an analog of compound (2)) can be carried out wherein the method further comprises one or more steps selected from: extraction of compound (2) or the analog of compound (2); isolation of compound (2) or the analog of compound (2); purification of compound (2) or the analog of compound (2); and crystallization of compound (2) or the analog of compound (2). Methods, techniques, and protocols for extracting, isolating, purifying, and/or crystallizing compound (2) or its analogs from biocatalytic reaction mixtures produced by the above disclosed methods are known to the ordinary artisan and/or accessed through routine experimentation. Additionally, illustrative methods are provided in the Examples below.

In some embodiments of the methods, the method can further comprise a step of dimethylating compound (2) or an analog of compound (2) thereby forming (S)-3-(1-(dimethylamino)ethyl)phenol (compound (3)), which is an intermediate in the preparation of the API rivastigmine, or an analog of compound (3)

This further dimethylation step is a variation on the chemical Eschweiler-Clark reductive alkylation using formic acid, formaldehyde, and triethylamine (TEA). However, whereas a classical Eschweiler-Clark reductive alkylation results in ˜85% conversion and ˜15% mass loss, it is a surprising result of method disclosed herein that the use of about 0.8 to about 1.6 equivalents of TEA results in >95% conversion of compound (2) to compound (3) with minimal formation of any ketone byproduct (e.g., compound (1)). Further exemplary materials and protocols that can be used in this dimethylation method are provided in Example 5 below. Accordingly, in embodiments of the methods, the method further comprises a step of dimethylation of compound (2) comprising contacting compound (2) or the analog of compound (2) with triethylamine, formic acid, and formaldehyde, under suitable reaction conditions. In some embodiments of this further dimethylation step the suitable reaction conditions comprise about 0.8 to about 1.6, about 1.0 to about 1.5, about 1.2 to about 1.4 equivalents, or about 1.3 equivalents of triethylamine. In some embodiments of this further dimethylation step the suitable reaction conditions comprise about 10 to about 18 equivalents, or 12 to 15 equivalents, or about 13.5 equivalents of formic acid. In some embodiments of this further dimethylation step the suitable reaction conditions comprise about 7 to about 9 equivalents, about 8 to about 9 equivalents, or about 9 equivalents of formaldehyde. In some embodiments of this further dimethylation step the suitable reaction conditions comprise at temperature of about 60° C. to about 90° C., about 70° C. to about 80° C., or about 75° C. In some embodiments, the method results in at least about 95%, 96%, 97%, 98%, 99% or greater conversion of compound (2) to dimethylated product of compound (3), and optionally less than about 1%, or even less than 0.5% of a ketone byproduct of compound (1). In some embodiments of this dimethylation step, the reaction conditions comprise about 1.3 equivalents of TEA, about 13.5 equivalents of formic acid, about 9 equivalents of formaldehyde, and a temperature of about 75° C., and result in at least about 98% or greater conversion of compound (2) to the dimethylated product of compound (3) and optionally about 0.5% or less of a ketone byproduct of compound (1).

In some embodiments, the engineered transaminase polypeptide can be used in a process for the preparation of the advanced pharmaceutical intermediate, rivastigmine (compound (4)), its salts, hydrates, or solvates.

Thus, in some embodiments, in a process for the preparation of the compound (4), a step in the process comprises contacting 3-hydroxyacetophenone (compound (1)) with a transaminase described herein in the presence of an amino donor under reaction conditions suitable for conversion of compound (1) to (S)-3-(1-aminoethyl)-phenol (compound (2)) in enantiomeric excess. Any of the conditions described above can be used in the process.

In some embodiments, the amino donor is isopropylamine (IPM), putrescine, L-lysine, ornithine, or D- or L-alanine. In some embodiments, the amino donor is isopropylamine.

Various features and embodiments of the disclosure are illustrated in the following representative examples, which are intended to be illustrative, and not limiting.

6. EXAMPLES Example 1 Synthesis, Optimization, and Screening Engineered Transaminase Polypeptides

Gene Synthesis and Optimization:

The polynucleotide sequence encoding the reported wild-type omega transaminase polypeptide from Vibrio fluvialis of SEQ ID NO: 2 was codon optimized resulting and synthesized as the gene of SEQ ID NO: 1. The synthetic gene of SEQ ID NO: 1 was cloned into a pCK110900 vector system (see e.g., US Patent Application Publication 20060195947, which is hereby incorporated by reference herein) and subsequently expressed in E. coli W3110fhuA. The E. coli W3110 expresses the transaminase polypeptides as an intracellular protein under the control of the lac promoter. The polypeptide accumulates primarily as a soluble cytosolic active enzyme. HTP assays used for primary screening were carried out using the cleared cell-lysate from expression of these E. coli W3110 cells (see below). The synthetic gene of SEQ ID NO: 1 was optimized for increased expression and thermostability by inserting following active and silent mutations which are described in U.S. application Ser. No. 12/684,864, filed Jan. 6, 2010, which is incorporated herein by reference: (a) A9T, c852t, and g861a (associated with increased expression); (b) F86Y, and M294V (associated with increased activity); and (c) N45H, V177L, R211K, S324G, T391A, g594c (associated with increased thermostability). This initial optimization resulted in the synthetic gene of SEQ ID NO: 3 (encoding the polypeptide of SEQ ID NO: 4) which was used as the starting backbone for further optimization to generate genes encoding the engineered transaminase polypeptides of SEQ ID NOs: 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, and 44, each of which is capable of converting compound (1) to compound (2) with improved enzyme properties relative to the polypeptides SEQ ID NOs: 2 and 4. Further optimization of the gene of SEQ ID NO: 3 was carried out using the standard methods of directed evolution via iterative variant library generation by gene synthesis followed by screening and sequencing of hits.

Production of Shake Flask Powders (SFP):

A shake-flask procedure was used to generate engineered transaminase polypeptide powders used in secondary screening assays or in the biocatalytic process disclosed herein. Shake flask powder (SFP) includes approximately 30% total protein and accordingly provide a more purified preparation of an engineered enzyme as compared to the cell lysate used in HTP assays. A single microbial colony of E. coli containing a plasmid encoding an engineered transaminase of interest is inoculated into 50 mL Luria Bertani broth containing 30 μg/ml chloramphenicol and 1% glucose. Cells are grown overnight (at least 16 hours) in an incubator at 30° C. with shaking at 250 rpm. The culture is diluted into 250 mL Terrific Broth (12 g/L bacto-tryptone, 24 g/L yeast extract, 4 mL/L glycerol, 65 mM potassium phosphate, pH 7.0, 1 mM MgSO₄) containing 30 μg/ml chloramphenicol, in a 1 liter flask to an optical density at 600 nm (OD600) of 0.2 and allowed to grow at 30° C. Expression of the transaminase gene is induced by addition of isopropyl-O-D-thiogalactoside (“IPTG”) to a final concentration of 1 mM when the OD600 of the culture is 0.6 to 0.8 and incubation is then continued overnight (at least 16 hours). Cells are harvested by centrifugation (5000 rpm, 15 min, 4° C.) and the supernatant discarded. The cell pellet is resuspended with an equal volume of cold (4° C.) 100 mM triethanolamine (chloride) buffer, pH 7.0 (optionally including 2 mM MgSO₄), and harvested by centrifugation as above. The washed cells are resuspended in two volumes of the cold triethanolamine (chloride) buffer and passed through a French Press twice at 12,000 psi while maintained at 4° C. Cell debris is removed by centrifugation (9000 rpm, 45 minutes, 4° C.). The clear lysate supernatant was collected and stored at −20° C. Lyophilization of frozen clear lysate provides a dry shake-flask powder of crude transaminase polypeptide. Alternatively, the cell pellet (before or after washing) can be stored at 4° C. or −80° C.

Production of Downstream Process (DSP) Powders:

DSP powders contains approximately 80% total protein and accordingly provide a more purified preparation of the engineered transaminase enzyme as compared to the cell lysate used in the high throughput assay. Larger-scale (˜100-120 g) fermentation of the engineered transaminase for production of DSP powders can be carried out as a short batch followed by a fed batch process according to standard bioprocess methods. Briefly, transaminase expression is induced by addition of IPTG to a final concentration of 1 mM. Following fermentation, the cells are harvested and resuspended in 100 mM Triethanolamine-H₂SO₄ buffer, then mechanically disrupted by homogenization. The cell debris and nucleic acid are flocculated with polyethylenimine (PEI) and the suspension clarified by centrifugation. The resulting clear supernatant is concentrated using a tangential cross-flow ultrafiltration membrane to remove salts and water. The concentrated and partially purified enzyme concentrate can then be dried in a lyophilizer and packaged (e.g., in polyethylene containers).

HTP Assay:

Primary screening used to guide optimization was carried out on a 200 volume in 96-well plate high-throughput (HTP) assay protocol using cell lysates as follows: 60 μL of a 5 M isopropylamine (TPM) stock solution in buffer (100 mM TEA-HCl pH=7.5)) was added to each well. A stock solution of 10 mM PLP in sterile water was then added (16 μL/well). Buffer (100 mM TEA-HCl pH=7.5) was dispensed (74 μL/well) to make up the final volume to 200 μL followed by the clear cell lysate (40 μL/well) containing the engineered polypeptide. Cells were lysed in 150 μL/well of Lysis Buffer (1 mg/mL lysozyme, 0.5 mg/mL PMBS in buffer containing 1 mM PLP). The HTP assay reaction was started by adding 10 μL/well of a substrate stock solution in DMSO (680 g/L). The general HTP assay reaction conditions (used in screening that included the engineered polypeptides of SEQ ID NO: 4, 6, 8 and 10) are: 200 μL total volume, 40 μL cell lysate, 1.5 M IPM, 1 mM PLP, 34 g/L substrate of compound (1), 100 mM TEA-HCl, 5% (v/v) DMSO, pH 7.5, 25° C., and 24 h reaction time. In the subsequent rounds of screening, which included the engineered polypeptides of SEQ ID NO: 14-44, the assay reaction conditions were modified with increased temperatures as follows: temperature increased to T=30° C., for screening including SEQ ID NO: 12; and temperature increased to T=45° C., for screening including polypeptides of SEQ ID NO: 14-44. Additionally, the HTP assay conditions used in screening the engineered polypeptides of SEQ ID NO: 18-44 were modified as follows: 10-30 g/L of the product of compound (2) added in the assay solution in order to provide further screening for increased tolerance of the polypeptide to the product compound. Additionally, the HTP assay conditions used in screening the engineered polypeptides of SEQ ID NO: 36-44 were modified as follows: buffer salt was switched to acetate.

SFP and DSP Assays:

In addition to the HTP assay for primary screening, in some cases secondary screening was carried using shake-flask powder (SFP) and/or downstream-processed (DSP) preparations of the engineered transaminase polypeptides of SEQ ID NO: 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, and 44. The general SFP assay and DSP assay reaction conditions were as follows: 27 g/L 3-hydroxyacetophenone, 20 g/L transaminase SFP or DSP powder, 1.5 M IPM-HCl, 1 mM PLP, 0.1 mM TEA-HCl buffer, pH 7.5, allowed to react at ambient temperature for 24-48 hours. This general protocol was used in the early rounds of screening that included the engineered polypeptides of SEQ ID NO: 4, 6, 8 and 10. In the next round of screening, which included the polypeptide of SEQ ID NO: 12, the assay reaction conditions were modified as follows: substrate loading increased to 30 g/L, and temperature increased to 30° C. In the next round of screening, which included the polypeptides of SEQ ID NO: 14-28, the assay reaction conditions were modified as follows: substrate loading increased to 50 g/L, engineered polypeptide loading increased to 5 g/L, and temperature increased to 45° C. In subsequent rounds of screening, which included the polypeptides of SEQ ID NO: 30-44, the assay reaction conditions were modified as follows: buffer salt switched to acetate, substrate loading increased to 65 g/L (with subsequent dosing to 100 g/L), and enzyme loading decreased to 3 g/L.

Assay Analysis:

After running the HTP, SFP, or DSP assays, as described above, the reaction solution is analyzed for the conversion of substrate of compound (1) to the product of compound (2) and/or enantiopurity of product by HPLC, as described in Example 2.

Additionally, measurement of percent conversion to product of HTP assay reaction solutions can be carried out as follows. Extract HTP reaction solution (200 μL) using 1.00 mL of MTBE containing 5% DEA. Analyze extracted organic phase by GC using the following instrumentation and parameters: Column. J&W Cyclosil; Temperature: 230° C. (isotherm); Pressure: 30 psi (cte); Retention times: chiral amine product, compound (2)=1.15 min; ketone substrate, compound (1)=1.33 min.

Example 2 Analytical Methods Useful for Assays and Monitoring of the Biocatalytic Conversion of Compound (1) to Compound (2) Using Engineered Transaminase Polypeptides

This Example provides illustrative analytical methods that can be used to monitor the course of the reactions used for the biocatalytic production of (S)-3-(1-aminoethyl)-phenol (compound (2)) as well as determine purity, identity, and % ee of the (S)-3-(1-aminoethyl)-phenol product.

A. HPLC Method for Determining Percent Conversion of Compound (1) to Compound (2) (Method 1)

Sample Preparation:

200 μL of the reaction mixture was sampled and added to 800 μL of methanol. The mixture was centrifuged for 1-2 min after which 25 μL of the supernatant was added to 425 μL of mobile phase (80% 20 mM NH₄HCO₃ pH 9.9, 20% MeCN) in a glass vial. The sample was analyzed on an Agilent 1200 HPLC system using the instrumental parameters below.

Instrumentation and Parameters:

Agilent 1200 HPLC system; Column: Phenomenex Gemini NX C18, 150×4.6 mm, 5 μm; Mobile phase: 80% 20 mM NH₄HCO₃ pH 9.9 (adjusted w/ammonia), 20% Acetonitrile; Run Time: 3 min; Flow Rate: 1.5 mL/min; UV Detection wavelength: 275 nm; Column Temperature: 30° C.; Retention times: (S)-3-(1-aminoethyl)-phenol=2.1 min; 3-hydroxyacetophenone=2.6 min

The response factor for (S)-3-(1-aminoethyl)-phenol to 3-hydroxyacetophenone was determined to be 1.1, based on the relative intensity of signals using a 1:1 molar ratio standard solution of the two compounds.

B. GC method for Determining Acetone Concentration (Method 2)

Sample Preparation:

100 μL of the reaction was sampled and added to 900 μL of methanol. The solution was centrifuged and 200 μL of the supernatant was analyzed for acetone content using the Agilent GC 6890N instrumentation and parameters below.

Instrumentation and Parameters:

Agilent GC 6890N; Column: Roticap Wax Capillary 50.0m×250 μm×0.25 μm; Gas flow: Helium split ratio 60:1, split flow 77.5 mL/min; Inlet Pressure: 22.4 psi; Column Pressure 6.0 psi; Helium Flow rate: 1.1 mL/min; Inlet Temperature: 180° C.; Detector Temperature: 200° C.; Injection volume: 1 μL; Run time: 6.71 min; Retention Time (Acetone)=3.98 min.

The following temperature program was used:

Oven Ramp ° C./min Next ° C. Hold Time (min) Run Time (min) Initial 65 0 0 Ramp 7 105 1 6.71

C. HPLC Method for Determining Percent Purity of the (S)-3-(1-aminoethyl)-Phenol Product (Method 3)

Sample Preparation:

30.0 mg of product was weighed into a 100 mL volumetric flask. 50 mL of mobile phase (80% 20 mM NH₄HCO₃ pH 10.0, 20% acetonitrile) was added and the solution was sonicated for 5 min. The volume was made up by the addition of more mobile phase. 2 mL of the solution was passed through a 0.45 μm nylon filter membrane into a 2 mL HPLC glass vial. 10 μL of the sample was injected onto an HPLC which had been equilibrated for at least 10 minutes and run according to the instrumental parameters below.

Instrumentation and Parameters:

Varian 920-LC series; Column: Phenomenex Gemini NX C18, 150×4.6 mm, 3 μm; Mobile phase A: 20 mM NH₄HCO₃ pH 10.0 (adjusted with ammonia); Mobile phase B: acetonitrile, HPLC grade; Detection wavelength: 275 nm; Column Temperature: 30° C.; Retention times: (S)-3-(1-aminoethyl)-phenol=3.0 min; 3-hydroxyacetophenone=4.0 min.

The column was run using the following elution program:

Time Flow rate (min) % A % B (mL/min) 0 80 20 1.0 6.0 80 20 1.0 7.0 90 10 1.0 7.5 90 10 1.0 8.0 5 95 1.0 9.0 5 95 1.0 9.5 80 20 1.0 12.0 80 20 1.0

D. Method for Determining % ee of the Product of Compound (2) (Method 4)

Sample Preparation:

2.0 mg of sample was weighed into a 2 mL glass vial. 1 mL of Mobile Phase was added and the solution was gently mixed. 10 μl was injected into the HPLC which has been equilibrated for 30 min and analyzed on an Agilent 1200 series HPLC system according to the parameters below.

Instrumentation and Parameters:

Agilent 1200 series HPLC system; Column: Astec Chirobiotic TAG, 250×4.6 mm, 5 μm; Mobile phase: Methanol/Acetic acid/Triethylamine, (100/0.2/0.1) v %; Flow rate: 1.2 mL/min; Detection wavelength: 274 nm; Column Temperature: 15° C.; Retention times: (R)-3-(1-aminoethyl)-phenol=10.36 min; (S)-3-(1-aminoethyl)-phenol=11.27 min.

E. LC/MS Method for Identification of Product of Compound (2) (Method 5)

Sample Preparation:

1.0 mg of sample was weighed into a 2 mL glass vial. 2 mL of a 50/50 mixture of acetonitrile/H₂O was added to the vial. Serial dilution was performed to obtain a concentration of about 1 ppm. The sample was analyzed on the HPLC/MS system according to the parameters described below.

HPLC/MS Instrumentation and HPLC Parameters:

Agilent HPLC system with Applied Biosystem 3200 MS; Column: Phenomenex Gemini C18, 50×4.6 mm, 5 μm; Mobile phase A: H₂O, 0.1% vol formic acid; Mobile phase B: acetonitrile, 0.1% vol formic acid; Detection wavelength: 275 nm; Column Temperature: 25° C.; Retention time: (S)-3-(1-aminoethyl)-phenol=˜0.75 min.

The column was run using the following elution program:

Time Flow rate (min) % A % B (mL/min) 0 95 5 1.0 10.0 5 95 1.0 11.0 5 95 1.0 12.0 95 5 1.0 15.0 95 5 1.0

MS Parameters:

Ion Source: Turbo Spray; Curtain Gas: 10.0 psi; Collision Gas: High; Ionspray Voltage: 5500.0 V; Temperature: 600° C.; Ion Source Gas 1: 50.0 psi; Ion Source Gas 2: 50.0 psi; Declustering Potential: 14.4 V; Entrance Potential: 5.0 V; Collision Energy: 12.0 eV; Collision Cell Exit Potential: 3.0 V.

Example 3 Biocatalytic Production of (S)-3-(1-aminoethyl)-phenol (Compound (2)) at 65 g Scale

A 2 L baffled reactor was equipped with an overhead stirrer fitted with a flat-blade impeller, a sparging tube hooked up to a nitrogen inlet and flow meter, outlet valve, and temperature probe. To a 50 mL bottle was added 5 g of the polypeptide of SEQ ID NO: 32 and 50 mL of 0.1 M TEA acetate buffer solution (pH 7.5). The contents of the bottle were gently mixed until most of the enzyme dissolved into solution. The reaction vessel was then charged with 200 mL of 5 M isopropylamine acetate, 270 mg of pyridoxal-5′-phosphate, and 600 mL of 0.1 M TEA acetate buffer solution (pH 7.5). The mixture was stirred at 150 rpm at 37° C. (internal temperature) while adding the buffer solution containing the enzyme. The solution was stirred for an additional 5-10 min prior to the addition of the substrate.

A total of 65 g of the 3-hydroxyacetophenone (compound (1)) substrate was charged to the stirred mixture as a powder. After addition of substrate was complete, the volume of the reaction was topped up to 1 L (if necessary) with the appropriate amount of 0.1 M TBA buffer, pH 7.5. The resulting slurry was stirred at 150 rpm at 37° C. (internal temperature). The temperature was monitored using an external temperature probe. The reaction was conducted under a constant nitrogen sweep of 5 L/min. Additional 5 M isopropylamine acetate (100 mL) was charged to the stirred mixture after 24 h and again after 48 h.

The reaction course was periodically followed by taking samples from the reaction mixture, quenching, and analyzing as described in Method 1. For the purposes of tracking the process, t=0 was set at the time at which substrate was added. After in-process analyses indicated >95% conversion (70 hours), the reaction mixture was taken for subsequent workup and isolation.

A typical kinetic profile of the reaction progress is shown in the table below:

Sample Time (h) % Conversion 0 0 0 1 3 20.9 2 6 31.4 3 7 36.4 4 24 72.1 5 45 92.0 6 69 97.6

A sample of the reaction mixture was subjected to the analytical method described in Method 2. It was found that the acetone content in the reaction after 70 hours was less than 0.01 wt %. The reaction mixture was cooled down to room temperature (=23° C.) and transferred to a 2 L beaker. The reactor was washed down with 50 mL deionized water which was added to the reaction mixture. The combined solution was filtered using filter paper and a Buchner funnel under house vacuum. The filter cake was washed with 50 mL of deionized water.

A 2 L reactor was charged with the filtered solution. 300 mL (5 vol) of MTBE was charged to the filtrate and the solution was stirred for 30 min at 150 rpm. After separation, the aqueous phase was collected and the pH of the aqueous layer was adjusted to 10.0-10.2 using 10 N NaOH. The resulting solution was concentrated by rotary evaporation (150 mmHg, 40° C.) for 1 hour after which the pH was readjusted to 10.0-10.2 using 10 N NaOH.

The solution was transferred to a 2 L reactor and heated to an internal temperature of 70° C. 100 g of sodium sulfate was added to the aqueous solution and which was agitated at 70° C. at 150 rpm for 10 minutes. 500 mL (8 vol) of isopropyl acetate (IPAc) was added and the mixture was agitated at 150 rpm at 70° C. for 30 minutes. The organic phase was separated and the process was repeated with the aqueous layer twice more. The organic phases from all extractions were combined, filtered, and concentrated under reduced pressure to a volume of ˜125 mL (2 vol).

A volume of 200 mL (3 vol) of heptanes was added and the resulting slurry was concentrated under reduced pressure to ˜125 mL (2 vol). A volume of 200 mL of heptanes was added a final time and the slurry was concentrated under reduced pressure to =125 mL after which the slurry was filtered and the filter cake washed with 50 mL of heptanes. The resulting solid was dried in the vacuum oven (2 mm Hg) at 25° C. for 24 h.

The reaction resulted in a total of 57.5 g (88.4% overall isolated yield) of (S)-3-(1-aminoethyl)-phenol (compound (2)) obtained with a chemical purity of 99.2% and an enantiomeric purity of 99.8% ee.

Example 4 Biocatalytic Production of (S)-3-(1-aminoethyl)-phenol (Compound (2)) at 100 g Scale

A. Biocatalytic Reaction

A 2 L jacketed reactor with baffle was equipped with an overhead stirrer fitted with a flat-blade impeller, a sparging tube hooked up to a nitrogen inlet and flow meter, outlet valve, and temperature probe. The reactor was charged sequentially with the following: 300 mL of 0.1 M TEA acetate buffer solution (pH 7.5); 588 mL of 5 M isopropylamine (IPM) acetate solution; 0.27 g of pyridoxal-5′-phosphate in 20 mL of the buffer solution; and 40 g of the 3-hydroxyacetophenone (compound (1)) substrate. This reaction mixture was stirred at 45° C. (internal temperature) at 150 rpm with a nitrogen flow rate of 5 L/min until all the substrate dissolved into solution. The pH of the reaction was adjusted to 7.4-7.5 using 2.5 N NaOH and the remainder of the reaction volume was made up to 1 L with 0.1 M TEA buffer. The reaction mixture was then charged sequentially with 3 g of the polypeptide of SEQ ID NO: 32 in 30 mL buffer solution, and 60 g of the of the 3-hydroxyacetophenone (compound (1)) substrate in 147 mL in 5 M IPM acetate solution. The substrate solution was added at a rate of 4 g/L/hr. The reaction volume was maintained between 1.0-1.1 L by the continuous addition of deionized water once all of the substrate had been added. The reaction mixture was stirred at the above conditions for 36 hours.

The reaction course was periodically followed by taking samples from the reaction mixture, quenching, and analyzing as described in Method 1. Samples were also frequently monitored for acetone content using the procedure described in Method 2. For the purposes of tracking the process, t=0 was set at the time at which the enzyme was added. After in-process analyses indicated ˜95% conversion (32 hours), the reaction mixture was taken for subsequent workup and isolation. A typical reaction profile is shown in the table below:

% Acetone Sample Time (h) Conversion Conc (mM) 0 0 0 — 1 2 24.3 35.2 2 4 35.7 44.2 3 18 81.7 8.2 4 24 90.1 6.0 5 32 94.7 2.9

B. Product Work-Up and Isolation

The reaction mixture was cooled down to room temperature (˜23° C.) and transferred to a 2 L beaker. The reactor was washed down with 50 mL of deionized water and collected separately. The reaction mixture was filtered using filter paper and Buchner funnel under house vacuum and the filter cake was washed with the collected 50 mL of deionized water.

300 mL (3 vol) of MTBE was added to the filtrate and the solution was stirred for 30 min at 150 rpm. The layers were separated and the aqueous phase was collected. The aqueous layer was stirred at 100 rpm using a mechanical stirrer and the pH was slowly adjusted to first 9.5 and then to 10.0-10.2 over a period of 1-2 hr using 10 N NaOH. The resulting solution was concentrated under reduced pressure (80 mmHg, 40° C.) for 1 hour after which the pH was readjusted to 10-10.2 using 10 N NaOH. After stirring for 30 min, the solution was concentrated again under the same conditions. The resulting pH was adjusted to ensure a final pH of 9.75-10.5 and a final volume of 0.9-1.0 L.

The resulting slurry was cooled down to room temperature (˜23° C.) and stirred at 50 rpm for 3 h. Afterwards, the solid was filtered off and the filter cake was washed with 100 mL of cold water. The filter cake was dried in the vacuum oven (3-20 mm Hg) at 35° C. for 24 h.

89 g (88.3% isolated yield) of the (S)-3-(1-aminoethyl)phenol product (compound (2)) was isolated with a chemical purity of 99.0% and >99.8% ee.

Example 5 Chemical Conversion of (S)-3-(1-aminoethyl)-phenol (Compound (2)) to (S)-3-(1-(dimethylamino)ethyl)phenol (Compound (3)) at 12 g Scale

A. Chemical Reaction

A 300 mL jacketed reactor was charged sequentially with 60 mL formaldehyde and 21 mL formic acid. The reaction mixture was stirred for 10 min at 25° C. (internal temperature) at 200 rpm under a nitrogen atmosphere. The reaction mixture was then charged with 16.4 mL triethylamine (1.3 equivalents) over 30 minutes (added at 33 mL/h) under an atmosphere of nitrogen. The reaction mixture was heated to 75° C. (internal temperature) at 200 rpm under a nitrogen atmosphere. The reaction mixture was then charged with 12 g of (S)-3-(1-aminoethyl)phenol (Compound (2)) dissolved in 24 mL of formic acid (˜36 mL total) over 1 h (added at 36 mL/h). This reaction mixture was stirred at 75° C. (internal temperature) at 200 rpm under a nitrogen atmosphere for 4 h.

The reaction course was followed by taking samples from the reaction mixture, quenching, and analyzing using HPLC. HPLC samples were prepared by taking from the reaction vessel, a sample of 10 μL is added into a HPLC vial and 0.98 mL of acetonitrile: buffer mixture (1:1) were added (50 times dilution). The HPLC sample was centrifuged for 1-2 min after which 25 μL of the supernatant was added to 425 μL of mobile phase (80% 20 mM NH₄HCO₃ pH 9.9, 20% MeCN) in a glass vial.

The HPLC sample was analyzed on an Agilent 1200 HPLC system using the following instrumental parameters: Phenomenex Gemini NX C18, 150×4.6 mm, 5 μm column; Mobile phase: 80% 20 mM NH₄HCO₃ pH 9.9 (adjusted w/ammonia), 20% Acetonitrile; Injection volume: 10 μL; Run Time: 8.00 min; Flow Rate: 1.50 mL/min; UV Detection wavelength: 275 nm; Column Temperature: 30° C.; Retention times: (S)-3-(1-aminoethyl)-phenol=1.85 min; 3-hydroxyacetophenone=2.41 min; (S)-3-(1-(dimethylamino)ethyl)phenol=1.1 min. The response factor for (S)-3-(1-aminoethyl)-phenol to 3-hydroxyacetophenone was determined to be 1.1, based on the relative intensity of signals using a 1:1 molar ratio standard solution of the two compounds.

For the purposes of tracking the process, t=0 was set at the time at which the substrate was added. A typical reaction profile is shown in the table below:

Time % Conversion to % ketone by-product (h) Compound (3) (Compound (1)) 0 0 — 1 92 ~0.5 3 97 ~0.5 5 99 ~0.5

B. Product Work-Up and Isolation

After in-process analyses indicated ˜99% conversion (5 h), the reaction mixture, which was a dark yellow solution, was taken for subsequent workup and isolation.

The reaction mixture was cooled down to 25° C. (internal temperature) and transferred to 500 mL round bottom flask and concentrated under reduced pressure (80 mmHg, 55° C.) for 1 h. After the evaporation, 25 mL of toluene was charged and then concentrated again under the same conditions for 1 h. Then, the reaction mixture was transferred to a 300 mL jacked reactor and cooled down to 10˜15° C. (internal temperature).

The reaction mixture was stirred at 200 rpm using a mechanical stirrer and the pH was slowly adjusted to 10.0 using ˜50 mL of 10 N NaOH. Then, the reaction mixture was heated to 70° C. (internal temperature) and if required, extra 10N—NaOH solution was charged to maintained pH 10. 50 mL of isopropyl acetate (IPAc) was charged into the reaction mixture and stirred for 30 min. The phases were allowed to separate, and then both layers were collected separately. The aqueous layer was charged back to a 300 mL jacketed flask, 50 mL of IPAc was charged into the jacketed flask, stirred for 30 min, and the phases were allowed to separate.

The combined organic layers were charged to a 300 mL jacketed flask and stirred for 18 h at 200 rpm after charging 2.4 g of activated carbon at room temperature (˜23° C.). The resulting solution was filtered through filter paper and filtered activated carbon was washed with 10 mL of IPAc. The combined organic solution was concentrated under reduced pressure (95 mmHg, 40° C.) till approx 1 volume of IPAc remains in the mass.

The concentrated organic layer was agitated for 1 h at 25° C. under an atmosphere of nitrogen with 200 rpm. The solid was filtered off and the filter cake was washed with chilled IPAc (0° C., 5 mL). The filter cake was dried in the vacuum oven (3-20 mm Hg) at 35° C. for 24 h.

A total of 13 g (90% isolated yield) of (S)-3-(1-(dimethylamino)ethyl)phenol (compound (3)) was isolated with a chemical purity of ˜99.5% by normalization.

All publications, patents, patent applications and other documents cited in this application are hereby incorporated by reference in their entireties for all purposes to the same extent as if each individual publication, patent, patent application or other document were individually indicated to be incorporated by reference for all purposes.

While various specific embodiments have been illustrated and described, it will be appreciated that various changes can be made without departing from the spirit and scope of the invention(s). 

What is claimed is:
 1. An engineered transaminase polypeptide capable of converting 3-hydroxyacetophenone (compound (1)) to (S)-3-(1-aminoethyl)-phenol (compound (2)),

the transaminase polypeptide comprising an amino acid sequence having at least 80% sequence identity to SEQ ID NO:2 and amino acid residue differences as compared to SEQ ID NO:2 at one or more positions selected from X18, X163, X235, X244, X323, X383, X424, and X427.
 2. The polypeptide of claim 1 in which the transaminase polypeptide has at least 1.2 times the activity of SEQ ID NO:2 in the rate of conversion of 3-hydroxyacetophenone to (S)-3-(1-aminoethyl)-phenol under reaction conditions of 35 g/L of 3-hydroxyacetophenone, 1.5 M isopropylamine, 1 mM pyridoxal phosphate, 5% v/v DMSO, pH 7.5, and 45° C.
 3. The polypeptide of claim 1 in which the amino acid residue differences as compared to SEQ ID NO: 2 are selected from the following: residue at position X18 is A; residue at position X163 is F or H; residue at position X235 is P; residue at position X244 is T; residue at position X323 is T; residue at position X383 is V; residue at position X424 is A; and residue at position X427 is Y.
 4. The polypeptide of claim 1 or 3 in which the transaminase polypeptide amino acid sequence has additional amino acid residue differences as compared to SEQ ID NO:2 at one or more of the following positions: X21, X31, X74; X113, X122, X130, X133, X146, X147, X153, X164, X167, X168, X174, X233, X245, X286, X293, X315, X316, X318, X332, X375, X394, and X418.
 5. The polypeptide of claim 4 in which the additional amino acid residue differences as compared to SEQ ID NO: 2 are selected from the following: residue at position X21 is T; residue at position X31 is M; residue at position X74 is T; residue at position X113 is V; residue at position X122 is E; residue at position X130 is L or M; residue at position X133 is R; residue at position X146 is L; residue at position X147 is K; residue at position X153 is S; residue at position X164 is S or G; residue at position X167 is K; residue at position X168 is D or K; residue at position X174 is E; residue at position X233 is T or I; residue at position X245 is T; residue at position X286 is S; residue at position X293 is S; residue at position X312 is D; residue at position X315 is G; residue at position X316 is H; residue at position X318 is D; residue at position X332 is T; residue at position X375 is V; residue at position X394 is G; and residue at position X418 is Q.
 6. The polypeptide of claim 1 in which the polypeptide amino acid sequence comprises at least the following amino acid difference as compared to SEQ ID NO: 2: residue at position X163 is F or H.
 7. The polypeptide of claim 5 in which the polypeptide amino acid sequence comprises at least the following amino acid residue differences as compared to SEQ ID NO:2: residue at position X153 is S; and residue at position X233 is I.
 8. The polypeptide of claim 5 in which the polypeptide amino acid sequence comprises at least the following amino acid residue differences as compared to SEQ ID NO:2: residue at position X153 is S; residue at position X163 is F or H; and residue at position X233 is T or I.
 9. The polypeptide of claim 5 in which the polypeptide amino acid sequence has at least the following amino acid residue differences as compared to SEQ ID NO:2: residue at position X153 is S; residue at position X163 is F or H; residue at position X233 is T or I; residue at position X235 is P; residue at position X424 is A; and residue at position X427 is Y.
 10. The polypeptide of claim 5 in which the polypeptide amino acid sequence has at least the following amino acid residue differences as compared to SEQ ID NO:2: residue at position X18 is A; residue at position X21 is H; residue at position X153 is S; residue at position X163 is F or H; residue at position X233 is T or I; residue at position X235 is P; residue at position X323 is T; residue at position X383 is V; residue at position X424 is A; and residue at position X427 is Y.
 11. The polypeptide of claim 5 in which the polypeptide amino acid sequence has at least the following amino acid residue differences as compared to SEQ ID NO:2: residue at position X18 is A; residue at position X21 is H; residue at position X147 is K; residue at position X153 is S; residue at position X163 is F or H; residue at position X233 is T or I; residue at position X235 is P; residue at position X244 is T; residue at position X323 is T; residue at position X383 is V; residue at position X424 is A; and residue at position X427 is Y.
 12. The polypeptide of claim 5 in which the polypeptide amino acid sequence has at least the following amino acid residue differences as compared to SEQ ID NO:2: residue at position X18 is A; residue at position X21 is H; residue at position X133 is R; residue at position X146 is L; residue at position X147 is K; residue at position X153 is S; residue at position X163 is F; residue at position X233 is T or I; residue at position X235 is P; residue at position X244 is T; residue at position X323 is T; residue at position X383 is V; residue at position X424 is A; and residue at position X427 is Y.
 13. The polypeptide of claim 5 in which the polypeptide amino acid sequence has at least the following amino acid residue differences as compared to SEQ ID NO:2: residue at position X18 is A; residue at position X21 is H; residue at position X31 is M; residue at position X133 is R; residue at position X146 is L; residue at position X147 is K; residue at position X153 is S; residue at position X163 is F or H; residue at position X233 is T or I; residue at position X235 is P; residue at position X244 is T; residue at position X318 is D; residue at position X323 is T; residue at position X383 is V; residue at position X424 is A; and residue at position X427 is Y.
 14. The polypeptide of any one of claims 1 to 13 in which the polypeptide amino acid sequence has additional amino acid residue differences as compared to SEQ ID NO:2 at one or more of the following positions: X9, X45, X86, X177, X211, X294, X324, and X391.
 15. The polypeptide of claim 14 in which the additional amino acid residue differences as compared to SEQ ID NO: 2 at one or more of positions X9, X45, X86, X177, X211, X294, X324, and X391 is selected from the following: residue at position X9 is T, residue at position X45 is H, residue at position X86 is Y, residue at position X177 is L; residue at position X211 is K, residue at position X294 is V, residue at position X324 is G, and residue at position X391 is A.
 16. The polypeptide of claim 14 in which the polypeptide amino acid sequence comprises at least the following amino acid residue differences as compared to SEQ ID NO:2: residue at position X153 is S; residue at position X177 is L; and residue at position X233 is T, or I.
 17. The polypeptide of claim 1 in which the polypeptide amino acid sequence comprises a sequence selected from the group consisting of SEQ ID NO: 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, and
 44. 18. A polynucleotide encoding the polypeptide of any one of claims 1 to
 17. 19. The polynucleotide of claim 18 in which the polynucleotide sequence comprises a sequence selected from the group consisting of SEQ ID NO: 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, and
 43. 20. An expression vector comprising the polynucleotide of claim 18 or
 19. 21. The expression vector of claim 20 comprising a control sequence.
 22. A host cell comprising the polynucleotide of claims 18 to 19 or the expression vector of any one of claims 20 to
 21. 23. A method for preparing a polypeptide of any one of claims 1 to 17 comprising culturing a host cell of claim 22 and isolating the polypeptide from the cell.
 24. A method for preparing (S)-3-(1-aminoethyl)-phenol (compound (2)) or an analog of compound (2) in enantiomeric excess,

comprising contacting 3-hydroxyacetophenone (compound (1)) or an analog of compound (1)

with a transaminase polypeptide of any one of claims 1 to 17 in the presence of an amino donor under suitable reactions conditions.
 25. The method of claim 24 in which the suitable reaction conditions comprise the amino donor at a concentration of at least about 0.5 M, at least about 1.0 M, at least about 2.5 M, at least about 5.0 M, at least about 7.5 M, at least about 10.0 M, or more.
 26. The method of claim 24 in which the amino donor is selected from the group consisting of isopropylamine, putrescine, L-lysine, D-ornithine, L-ornithine, D-alanine, L-alanine, and mixtures thereof.
 27. The method of claim 24 in which the amino donor is isopropylamine or isopropylamine acetate.
 28. The method of claim 24 in which the amino donor is isopropylamine acetate.
 29. The method of claim 27 which further comprises the removal of acetone formed from the isopropylamine.
 30. The method of claim 24 in which the suitable reaction conditions comprise a compound (1) loading of at least about 20 g/L, at least about 25 g/L, at least about 30 g/L, at least about 40 g/L, at least about 50 g/L, at least about 75 g/L, at least about 100 g/L, at least about 150 g/L, at least about 200 g/L, at least about 250 g/L, or even greater.
 31. The method of claim 24 in which the suitable reaction conditions comprise an engineered polypeptide concentration of about 0.1 to about 15 g/L, about 0.5 to about 10 g/L, about 1.0 to about 5 g/L, about 2 to about 5 g/L, about 15 g/L, about 10 g/L, about 5, g/L, about 3 g/L, about 2 g/L, about 1.5 g/L, about 1.0 g/L, about 0.75 g/L, or even lower concentration.
 32. The method of claim 24 in which the suitable reaction conditions comprise a temperature of about 15° C. to about 60° C., about 20° C. to about 55° C., about 30° C. to about 50° C., about 40° C. to about 60° C., about 40° C. to about 50° C., about 45° C. to about 55° C., about 25° C., about 30° C., about 35° C., about 40° C., about 45° C., about 50° C., about 55° C., or about 60° C., or more.
 33. The method of claim 24 in which the suitable reaction conditions comprise a pH of about 5.0 to about 11.0, a pH of about 6.0 to about 10.5, a pH of about 6.5 to about 10.0, a pH of about 7.0 to about 9.5, a pH of about 7.0 to about 9.0, a pH of about 7.0 to about 8.5, or a pH of about 7.2 to about 7.8, or about pH 7.5.
 34. The method of claim 24 in which the suitable reaction conditions comprise a buffer solution of about 0.05 M TEA to about 0.25 M TEA, or about 0.1 M TEA.
 35. The method of claim 24 in which the suitable reaction conditions comprise a substrate loading of compound (1) of at least about 20 g/L, 30 g/L, 40 g/L, 50 g/L, 60 g/L, 70 g/L, 100 g/L, or more, and wherein the method results in at least about 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or greater conversion of compound (1) to compound (2) in about 48 h or less, in about 36 h or less, or in about 24 h or less.
 36. The method of claim 35 in which the amino donor is isopropylamine or isopropylamine acetate at a concentration of at least about 0.5 M, at least about 1.0 M, at least about 2.5 M, at least about 5.0 M, at least about 7.5 M, at least about 10.0 M, or more.
 37. The method of claim 35 in which the suitable reaction conditions further comprise an engineered polypeptide concentration of about 0.1 to about 15 g/L, about 0.5 to about 10 g/L, about 1.0 to about 5 g/L, about 2 to about 5 g/L.
 38. The method of claim 24, wherein the method results in an enantiomeric excess of compound (2) of at least 97%, 98, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9%.
 39. The method of claim 24 in which the suitable reaction conditions comprise addition of the polypeptide to a solution having an initial substrate loading of at least about 20 g/L, 30 g/L, or 40 g/L, followed by addition of further substrate to the solution at a rate of about 4 g/L/h until a final substrate loading of at least about 30 g/L, 40 g/L, 50 g/L, 60 g/L, 70 g/L, 100 g/L or more, is reached.
 40. The method of claim 39 in which the further substrate added is in a solution comprising isopropylamine or isopropylamine acetate at a concentration of at least about 0.5 M, at least about 1.0 M, at least about 2.5 M, at least about 5.0 M, at least about 7.5 M, at least about 10.0 M.
 41. The method of claim 24 in which the method comprises contacting compound (1) with the transaminase polypeptide.
 42. The method of claim 24 in which the suitable reaction conditions comprise: (1) substrate loading of about 25-200 g/L compound (1); (2) polypeptide concentration of about 1.0-15 g/L; (3) IPM concentration of about 0.1-10 M; (4) PLP cofactor at a concentration of about 0.1-0.3 g/L; (5) about pH 5.0-10.0; and (6) temperature of about 30-60° C.
 43. The method of claim 24 in which the suitable reaction conditions comprise: (1) substrate loading of about 25-75 g/L compound (1); (2) polypeptide concentration of about 1.0-15 g/L; (3) IPM concentration of about 0.5-2.5 M; (4) PLP cofactor at a concentration of about 0.1-0.3 g/L; (5) about pH 7.0-8.0; and (6) temperature of about 35-45° C.
 44. The method of claim 24 in which the suitable reaction conditions comprise: (1) substrate loading of about 25-75 g/L compound (1); (2) polypeptide concentration of about 1.0-10 g/L; (3) IPM concentration of about 1.0-2.0 M; (4) PLP cofactor at a concentration of about 0.1-0.3 g/L; (5) about pH 7.2-7.8; and (6) temperature of about 35-45° C.
 45. The method of claim 24, wherein the analog of compound (1) is a compound of Formula I

wherein R is a hydroxyl protecting group, and whereby the analog of compound (2) prepared is a compound of Formula II


46. The method of any one of claims 24 to 45 in which the method further comprises one or more steps selected from: extraction of compound (2) or the analog of compound (2); isolation of compound (2) or the analog of compound (2); purification of compound (2) or the analog of compound (2); and crystallization of compound (2) or the analog of compound (2).
 47. The method of any one of claims 24 to 45 in which the method further comprises a step of dimethylating compound (2) or an analog of compound (2) thereby forming compound (3) or an analog of compound (3)


48. The method of claim 47 in which the demethylating step comprises contacting compound (2), or the analog of compound (2), with triethylamine, formic acid, and formaldehyde, under suitable reaction conditions.
 49. The method of claim 48 in which the suitable reaction conditions comprise about 0.8 to about 1.6, about 1.0 to about 1.5, about 1.2 to about 1.4 equivalents, or about 1.3 equivalents of triethylamine.
 50. The method of claim 48 in which the suitable reaction conditions comprise about 10 to about 18 equivalents, or 12 to 15 equivalents, or about 13.5 equivalents of formic acid.
 51. The method of claim 48 in which the suitable reaction conditions comprise about 7 to about 9 equivalents, about 8 to about 9 equivalents, or about 9 equivalents of formaldehyde.
 52. The method of claim 48 in which the suitable reaction conditions comprise at temperature of about 60° C. to about 90° C., about 70° C. to about 80° C., or about 75° C.
 53. The method of claim 48 in which the method results in at least about 95%, 96%, 97%, 98%, 99% or greater conversion of compound (2) to compound (3).
 54. The method of any one of claims 47 to 49 in which the method further comprises one or more steps selected from: extraction of compound (3) or the analog of compound (3); isolation of compound (3) or the analog of compound (3); purification of compound (3) or the analog of compound (3); and crystallization of compound (3) or the analog of compound (3).
 55. A process for the preparation of compound (4) in enantiomeric excess,

wherein a step in the process comprises contacting 3-hydroxyacetophenone (compound (1)) or an analog of compound (1)

with a transaminase polypeptide of any one of claims 1 to 17 in the presence of an amino donor under suitable reactions conditions for conversion of the compound (1) to (5)-3-(1-aminoethyl)-phenol (compound (2)) or an analog of compound (2)


56. The process of claim 55 in which the step in the process comprises contacting compound (1) with the transaminase polypeptide.
 57. The process of claim 55 in which the amino donor is isopropylamine.
 58. The method of any one of claims 24 to 57 in which the polypeptide comprises an amino acid sequence selected from the group consisting of SEQ ID NO: 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, and
 44. 